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annotate docker/alphafold/README.md @ 1:6c92e000d684 draft

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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
author galaxy-australia
date Tue, 01 Mar 2022 02:53:05 +0000
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1 ![header](imgs/header.jpg)
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3 # AlphaFold
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5 This package provides an implementation of the inference pipeline of AlphaFold
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6 v2.0. This is a completely new model that was entered in CASP14 and published in
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7 Nature. For simplicity, we refer to this model as AlphaFold throughout the rest
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8 of this document.
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10 We also provide an implementation of AlphaFold-Multimer. This represents a work
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11 in progress and AlphaFold-Multimer isn't expected to be as stable as our monomer
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12 AlphaFold system.
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13 [Read the guide](#updating-existing-alphafold-installation-to-include-alphafold-multimers)
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14 for how to upgrade and update code.
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16 Any publication that discloses findings arising from using this source code or the model parameters should [cite](#citing-this-work) the
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17 [AlphaFold paper](https://doi.org/10.1038/s41586-021-03819-2) and, if
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18 applicable, the [AlphaFold-Multimer paper](https://www.biorxiv.org/content/10.1101/2021.10.04.463034v1).
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20 Please also refer to the
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21 [Supplementary Information](https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-021-03819-2/MediaObjects/41586_2021_3819_MOESM1_ESM.pdf)
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22 for a detailed description of the method.
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24 **You can use a slightly simplified version of AlphaFold with
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25 [this Colab
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26 notebook](https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb)**
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27 or community-supported versions (see below).
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29 ![CASP14 predictions](imgs/casp14_predictions.gif)
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31 ## First time setup
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33 The following steps are required in order to run AlphaFold:
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35 1. Install [Docker](https://www.docker.com/).
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36 * Install
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37 [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html)
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38 for GPU support.
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39 * Setup running
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40 [Docker as a non-root user](https://docs.docker.com/engine/install/linux-postinstall/#manage-docker-as-a-non-root-user).
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41 1. Download genetic databases (see below).
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42 1. Download model parameters (see below).
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43 1. Check that AlphaFold will be able to use a GPU by running:
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45 ```bash
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46 docker run --rm --gpus all nvidia/cuda:11.0-base nvidia-smi
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47 ```
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49 The output of this command should show a list of your GPUs. If it doesn't,
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50 check if you followed all steps correctly when setting up the
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51 [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html)
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52 or take a look at the following
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53 [NVIDIA Docker issue](https://github.com/NVIDIA/nvidia-docker/issues/1447#issuecomment-801479573).
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54
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55 If you wish to run AlphaFold using Singularity (a common containerization platform on HPC systems) we recommend using some of the
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56 third party Singularity setups as linked in
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57 https://github.com/deepmind/alphafold/issues/10 or
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58 https://github.com/deepmind/alphafold/issues/24.
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59
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60 ### Genetic databases
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62 This step requires `aria2c` to be installed on your machine.
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64 AlphaFold needs multiple genetic (sequence) databases to run:
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66 * [BFD](https://bfd.mmseqs.com/),
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67 * [MGnify](https://www.ebi.ac.uk/metagenomics/),
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68 * [PDB70](http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/),
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69 * [PDB](https://www.rcsb.org/) (structures in the mmCIF format),
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70 * [PDB seqres](https://www.rcsb.org/) – only for AlphaFold-Multimer,
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71 * [Uniclust30](https://uniclust.mmseqs.com/),
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72 * [UniProt](https://www.uniprot.org/uniprot/) – only for AlphaFold-Multimer,
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73 * [UniRef90](https://www.uniprot.org/help/uniref).
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74
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75 We provide a script `scripts/download_all_data.sh` that can be used to download
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76 and set up all of these databases:
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78 * Default:
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80 ```bash
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81 scripts/download_all_data.sh <DOWNLOAD_DIR>
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82 ```
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83
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84 will download the full databases.
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86 * With `reduced_dbs`:
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87
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88 ```bash
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89 scripts/download_all_data.sh <DOWNLOAD_DIR> reduced_dbs
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90 ```
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91
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92 will download a reduced version of the databases to be used with the
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93 `reduced_dbs` database preset.
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94
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95 :ledger: **Note: The download directory `<DOWNLOAD_DIR>` should _not_ be a
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96 subdirectory in the AlphaFold repository directory.** If it is, the Docker build
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97 will be slow as the large databases will be copied during the image creation.
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98
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99 We don't provide exactly the database versions used in CASP14 – see the [note on
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100 reproducibility](#note-on-reproducibility). Some of the databases are mirrored
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101 for speed, see [mirrored databases](#mirrored-databases).
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102
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103 :ledger: **Note: The total download size for the full databases is around 415 GB
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104 and the total size when unzipped is 2.2 TB. Please make sure you have a large
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105 enough hard drive space, bandwidth and time to download. We recommend using an
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106 SSD for better genetic search performance.**
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107
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108 The `download_all_data.sh` script will also download the model parameter files.
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109 Once the script has finished, you should have the following directory structure:
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110
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111 ```
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112 $DOWNLOAD_DIR/ # Total: ~ 2.2 TB (download: 438 GB)
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113 bfd/ # ~ 1.7 TB (download: 271.6 GB)
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114 # 6 files.
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115 mgnify/ # ~ 64 GB (download: 32.9 GB)
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116 mgy_clusters_2018_12.fa
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117 params/ # ~ 3.5 GB (download: 3.5 GB)
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118 # 5 CASP14 models,
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119 # 5 pTM models,
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120 # 5 AlphaFold-Multimer models,
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121 # LICENSE,
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122 # = 16 files.
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123 pdb70/ # ~ 56 GB (download: 19.5 GB)
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124 # 9 files.
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125 pdb_mmcif/ # ~ 206 GB (download: 46 GB)
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126 mmcif_files/
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127 # About 180,000 .cif files.
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128 obsolete.dat
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129 pdb_seqres/ # ~ 0.2 GB (download: 0.2 GB)
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130 pdb_seqres.txt
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131 small_bfd/ # ~ 17 GB (download: 9.6 GB)
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132 bfd-first_non_consensus_sequences.fasta
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133 uniclust30/ # ~ 86 GB (download: 24.9 GB)
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134 uniclust30_2018_08/
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135 # 13 files.
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136 uniprot/ # ~ 98.3 GB (download: 49 GB)
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137 uniprot.fasta
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138 uniref90/ # ~ 58 GB (download: 29.7 GB)
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139 uniref90.fasta
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140 ```
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141
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142 `bfd/` is only downloaded if you download the full databases, and `small_bfd/`
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143 is only downloaded if you download the reduced databases.
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144
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145 ### Model parameters
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146
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147 While the AlphaFold code is licensed under the Apache 2.0 License, the AlphaFold
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148 parameters are made available for non-commercial use only under the terms of the
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149 CC BY-NC 4.0 license. Please see the [Disclaimer](#license-and-disclaimer) below
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150 for more detail.
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151
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152 The AlphaFold parameters are available from
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153 https://storage.googleapis.com/alphafold/alphafold_params_2021-10-27.tar, and
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154 are downloaded as part of the `scripts/download_all_data.sh` script. This script
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155 will download parameters for:
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156
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157 * 5 models which were used during CASP14, and were extensively validated for
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158 structure prediction quality (see Jumper et al. 2021, Suppl. Methods 1.12
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159 for details).
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160 * 5 pTM models, which were fine-tuned to produce pTM (predicted TM-score) and
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161 (PAE) predicted aligned error values alongside their structure predictions
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162 (see Jumper et al. 2021, Suppl. Methods 1.9.7 for details).
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163 * 5 AlphaFold-Multimer models that produce pTM and PAE values alongside their
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164 structure predictions.
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165
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166 ### Updating existing AlphaFold installation to include AlphaFold-Multimers
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167
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168 If you have AlphaFold v2.0.0 or v2.0.1 you can either reinstall AlphaFold fully
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169 from scratch (remove everything and run the setup from scratch) or you can do an
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170 incremental update that will be significantly faster but will require a bit more
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171 work. Make sure you follow these steps in the exact order they are listed below:
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172
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173 1. **Update the code.**
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174 * Go to the directory with the cloned AlphaFold repository and run
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175 `git fetch origin main` to get all code updates.
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176 1. **Download the UniProt and PDB seqres databases.**
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177 * Run `scripts/download_uniprot.sh <DOWNLOAD_DIR>`.
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178 * Remove `<DOWNLOAD_DIR>/pdb_mmcif`. It is needed to have PDB SeqRes and
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179 PDB from exactly the same date. Failure to do this step will result in
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180 potential errors when searching for templates when running
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181 AlphaFold-Multimer.
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182 * Run `scripts/download_pdb_mmcif.sh <DOWNLOAD_DIR>`.
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183 * Run `scripts/download_pdb_seqres.sh <DOWNLOAD_DIR>`.
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184 1. **Update the model parameters.**
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185 * Remove the old model parameters in `<DOWNLOAD_DIR>/params`.
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186 * Download new model parameters using
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187 `scripts/download_alphafold_params.sh <DOWNLOAD_DIR>`.
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188 1. **Follow [Running AlphaFold](#running-alphafold).**
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189
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190 #### API changes between v2.0.0 and v2.1.0
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191
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192 We tried to keep the API as much backwards compatible as possible, but we had to
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193 change the following:
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194
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195 * The `RunModel.predict()` now needs a `random_seed` argument as MSA sampling
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196 happens inside the Multimer model.
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197 * The `preset` flag in `run_alphafold.py` and `run_docker.py` was split into
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198 `db_preset` and `model_preset`.
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199 * The models to use are not specified using `model_names` but rather using the
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200 `model_preset` flag. If you want to customize which models are used for each
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201 preset, you will have to modify the the `MODEL_PRESETS` dictionary in
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202 `alphafold/model/config.py`.
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203 * Setting the `data_dir` flag is now needed when using `run_docker.py`.
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204
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205
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206 ## Running AlphaFold
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207
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208 **The simplest way to run AlphaFold is using the provided Docker script.** This
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209 was tested on Google Cloud with a machine using the `nvidia-gpu-cloud-image`
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210 with 12 vCPUs, 85 GB of RAM, a 100 GB boot disk, the databases on an additional
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211 3 TB disk, and an A100 GPU.
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212
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213 1. Clone this repository and `cd` into it.
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214
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215 ```bash
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216 git clone https://github.com/deepmind/alphafold.git
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217 ```
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218
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219 1. Build the Docker image:
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220
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221 ```bash
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222 docker build -f docker/Dockerfile -t alphafold .
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223 ```
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224
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225 1. Install the `run_docker.py` dependencies. Note: You may optionally wish to
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226 create a
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227 [Python Virtual Environment](https://docs.python.org/3/tutorial/venv.html)
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228 to prevent conflicts with your system's Python environment.
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229
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230 ```bash
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231 pip3 install -r docker/requirements.txt
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232 ```
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233
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234 1. Run `run_docker.py` pointing to a FASTA file containing the protein
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235 sequence(s) for which you wish to predict the structure. If you are
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236 predicting the structure of a protein that is already in PDB and you wish to
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237 avoid using it as a template, then `max_template_date` must be set to be
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238 before the release date of the structure. You must also provide the path to
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239 the directory containing the downloaded databases. For example, for the
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240 T1050 CASP14 target:
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241
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242 ```bash
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243 python3 docker/run_docker.py \
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244 --fasta_paths=T1050.fasta \
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245 --max_template_date=2020-05-14 \
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246 --data_dir=$DOWNLOAD_DIR
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247 ```
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248
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249 By default, Alphafold will attempt to use all visible GPU devices. To use a
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250 subset, specify a comma-separated list of GPU UUID(s) or index(es) using the
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251 `--gpu_devices` flag. See
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252 [GPU enumeration](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/user-guide.html#gpu-enumeration)
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253 for more details.
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254
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255 1. You can control which AlphaFold model to run by adding the
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256 `--model_preset=` flag. We provide the following models:
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257
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258 * **monomer**: This is the original model used at CASP14 with no ensembling.
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259
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260 * **monomer\_casp14**: This is the original model used at CASP14 with
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261 `num_ensemble=8`, matching our CASP14 configuration. This is largely
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262 provided for reproducibility as it is 8x more computationally
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263 expensive for limited accuracy gain (+0.1 average GDT gain on CASP14
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264 domains).
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265
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266 * **monomer\_ptm**: This is the original CASP14 model fine tuned with the
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267 pTM head, providing a pairwise confidence measure. It is slightly less
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268 accurate than the normal monomer model.
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269
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270 * **multimer**: This is the [AlphaFold-Multimer](#citing-this-work) model.
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271 To use this model, provide a multi-sequence FASTA file. In addition, the
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272 UniProt database should have been downloaded.
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273
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274 1. You can control MSA speed/quality tradeoff by adding
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275 `--db_preset=reduced_dbs` or `--db_preset=full_dbs` to the run command. We
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276 provide the following presets:
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277
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278 * **reduced\_dbs**: This preset is optimized for speed and lower hardware
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279 requirements. It runs with a reduced version of the BFD database.
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280 It requires 8 CPU cores (vCPUs), 8 GB of RAM, and 600 GB of disk space.
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281
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282 * **full\_dbs**: This runs with all genetic databases used at CASP14.
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283
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284 Running the command above with the `monomer` model preset and the
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285 `reduced_dbs` data preset would look like this:
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286
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287 ```bash
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288 python3 docker/run_docker.py \
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289 --fasta_paths=T1050.fasta \
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290 --max_template_date=2020-05-14 \
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291 --model_preset=monomer \
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292 --db_preset=reduced_dbs \
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293 --data_dir=$DOWNLOAD_DIR
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294 ```
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295
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296 ### Running AlphaFold-Multimer
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297
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298 All steps are the same as when running the monomer system, but you will have to
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299
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300 * provide an input fasta with multiple sequences,
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301 * set `--model_preset=multimer`,
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302 * optionally set the `--is_prokaryote_list` flag with booleans that determine
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303 whether all input sequences in the given fasta file are prokaryotic. If that
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304 is not the case or the origin is unknown, set to `false` for that fasta.
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305
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306 An example that folds a protein complex `multimer.fasta` that is prokaryotic:
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307
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308 ```bash
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309 python3 docker/run_docker.py \
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310 --fasta_paths=multimer.fasta \
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311 --is_prokaryote_list=true \
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312 --max_template_date=2020-05-14 \
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313 --model_preset=multimer \
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314 --data_dir=$DOWNLOAD_DIR
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315 ```
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316
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317 ### Examples
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318
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319 Below are examples on how to use AlphaFold in different scenarios.
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320
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321 #### Folding a monomer
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322
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323 Say we have a monomer with the sequence `<SEQUENCE>`. The input fasta should be:
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324
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325 ```fasta
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326 >sequence_name
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327 <SEQUENCE>
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328 ```
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329
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330 Then run the following command:
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331
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332 ```bash
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333 python3 docker/run_docker.py \
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334 --fasta_paths=monomer.fasta \
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335 --max_template_date=2021-11-01 \
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336 --model_preset=monomer \
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337 --data_dir=$DOWNLOAD_DIR
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338 ```
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339
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340 #### Folding a homomer
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341
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342 Say we have a homomer from a prokaryote with 3 copies of the same sequence
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343 `<SEQUENCE>`. The input fasta should be:
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344
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345 ```fasta
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346 >sequence_1
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347 <SEQUENCE>
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348 >sequence_2
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349 <SEQUENCE>
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350 >sequence_3
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351 <SEQUENCE>
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352 ```
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353
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354 Then run the following command:
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355
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356 ```bash
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
357 python3 docker/run_docker.py \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
358 --fasta_paths=homomer.fasta \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
359 --is_prokaryote_list=true \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
360 --max_template_date=2021-11-01 \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
361 --model_preset=multimer \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
362 --data_dir=$DOWNLOAD_DIR
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
363 ```
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
364
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
365 #### Folding a heteromer
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
366
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
367 Say we have a heteromer A2B3 of unknown origin, i.e. with 2 copies of
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
368 `<SEQUENCE A>` and 3 copies of `<SEQUENCE B>`. The input fasta should be:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
369
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
370 ```fasta
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
371 >sequence_1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
372 <SEQUENCE A>
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
373 >sequence_2
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
374 <SEQUENCE A>
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
375 >sequence_3
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
376 <SEQUENCE B>
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
377 >sequence_4
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
378 <SEQUENCE B>
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
379 >sequence_5
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
380 <SEQUENCE B>
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
381 ```
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
382
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
383 Then run the following command:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
384
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
385 ```bash
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
386 python3 docker/run_docker.py \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
387 --fasta_paths=heteromer.fasta \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
388 --is_prokaryote_list=false \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
389 --max_template_date=2021-11-01 \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
390 --model_preset=multimer \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
391 --data_dir=$DOWNLOAD_DIR
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
392 ```
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
393
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
394 #### Folding multiple monomers one after another
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
395
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
396 Say we have a two monomers, `monomer1.fasta` and `monomer2.fasta`.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
397
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
398 We can fold both sequentially by using the following command:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
399
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
400 ```bash
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
401 python3 docker/run_docker.py \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
402 --fasta_paths=monomer1.fasta,monomer2.fasta \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
403 --max_template_date=2021-11-01 \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
404 --model_preset=monomer \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
405 --data_dir=$DOWNLOAD_DIR
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
406 ```
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
407
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
408 #### Folding multiple multimers one after another
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
409
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
410 Say we have a two multimers, `multimer1.fasta` and `multimer2.fasta`. Both are
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
411 from a prokaryotic organism.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
412
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
413 We can fold both sequentially by using the following command:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
414
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
415 ```bash
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
416 python3 docker/run_docker.py \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
417 --fasta_paths=multimer1.fasta,multimer2.fasta \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
418 --is_prokaryote_list=true,true \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
419 --max_template_date=2021-11-01 \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
420 --model_preset=multimer \
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
421 --data_dir=$DOWNLOAD_DIR
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
422 ```
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
423
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
424 ### AlphaFold output
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
425
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
426 The outputs will be saved in a subdirectory of the directory provided via the
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
427 `--output_dir` flag of `run_docker.py` (defaults to `/tmp/alphafold/`). The
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
428 outputs include the computed MSAs, unrelaxed structures, relaxed structures,
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
429 ranked structures, raw model outputs, prediction metadata, and section timings.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
430 The `--output_dir` directory will have the following structure:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
431
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
432 ```
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
433 <target_name>/
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
434 features.pkl
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
435 ranked_{0,1,2,3,4}.pdb
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
436 ranking_debug.json
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
437 relaxed_model_{1,2,3,4,5}.pdb
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
438 result_model_{1,2,3,4,5}.pkl
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
439 timings.json
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
440 unrelaxed_model_{1,2,3,4,5}.pdb
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
441 msas/
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
442 bfd_uniclust_hits.a3m
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
443 mgnify_hits.sto
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
444 uniref90_hits.sto
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
445 ```
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
446
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
447 The contents of each output file are as follows:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
448
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
449 * `features.pkl` – A `pickle` file containing the input feature NumPy arrays
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
450 used by the models to produce the structures.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
451 * `unrelaxed_model_*.pdb` – A PDB format text file containing the predicted
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
452 structure, exactly as outputted by the model.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
453 * `relaxed_model_*.pdb` – A PDB format text file containing the predicted
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
454 structure, after performing an Amber relaxation procedure on the unrelaxed
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
455 structure prediction (see Jumper et al. 2021, Suppl. Methods 1.8.6 for
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
456 details).
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
457 * `ranked_*.pdb` – A PDB format text file containing the relaxed predicted
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
458 structures, after reordering by model confidence. Here `ranked_0.pdb` should
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
459 contain the prediction with the highest confidence, and `ranked_4.pdb` the
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
460 prediction with the lowest confidence. To rank model confidence, we use
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
461 predicted LDDT (pLDDT) scores (see Jumper et al. 2021, Suppl. Methods 1.9.6
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
462 for details).
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
463 * `ranking_debug.json` – A JSON format text file containing the pLDDT values
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
464 used to perform the model ranking, and a mapping back to the original model
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
465 names.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
466 * `timings.json` – A JSON format text file containing the times taken to run
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
467 each section of the AlphaFold pipeline.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
468 * `msas/` - A directory containing the files describing the various genetic
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
469 tool hits that were used to construct the input MSA.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
470 * `result_model_*.pkl` – A `pickle` file containing a nested dictionary of the
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
471 various NumPy arrays directly produced by the model. In addition to the
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
472 output of the structure module, this includes auxiliary outputs such as:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
473
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
474 * Distograms (`distogram/logits` contains a NumPy array of shape [N_res,
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
475 N_res, N_bins] and `distogram/bin_edges` contains the definition of the
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
476 bins).
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
477 * Per-residue pLDDT scores (`plddt` contains a NumPy array of shape
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
478 [N_res] with the range of possible values from `0` to `100`, where `100`
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
479 means most confident). This can serve to identify sequence regions
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
480 predicted with high confidence or as an overall per-target confidence
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
481 score when averaged across residues.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
482 * Present only if using pTM models: predicted TM-score (`ptm` field
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
483 contains a scalar). As a predictor of a global superposition metric,
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
484 this score is designed to also assess whether the model is confident in
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
485 the overall domain packing.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
486 * Present only if using pTM models: predicted pairwise aligned errors
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
487 (`predicted_aligned_error` contains a NumPy array of shape [N_res,
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
488 N_res] with the range of possible values from `0` to
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
489 `max_predicted_aligned_error`, where `0` means most confident). This can
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
490 serve for a visualisation of domain packing confidence within the
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
491 structure.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
492
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
493 The pLDDT confidence measure is stored in the B-factor field of the output PDB
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
494 files (although unlike a B-factor, higher pLDDT is better, so care must be taken
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
495 when using for tasks such as molecular replacement).
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
496
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
497 This code has been tested to match mean top-1 accuracy on a CASP14 test set with
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
498 pLDDT ranking over 5 model predictions (some CASP targets were run with earlier
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
499 versions of AlphaFold and some had manual interventions; see our forthcoming
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
500 publication for details). Some targets such as T1064 may also have high
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
501 individual run variance over random seeds.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
502
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
503 ## Inferencing many proteins
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
504
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
505 The provided inference script is optimized for predicting the structure of a
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
506 single protein, and it will compile the neural network to be specialized to
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
507 exactly the size of the sequence, MSA, and templates. For large proteins, the
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
508 compile time is a negligible fraction of the runtime, but it may become more
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
509 significant for small proteins or if the multi-sequence alignments are already
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
510 precomputed. In the bulk inference case, it may make sense to use our
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
511 `make_fixed_size` function to pad the inputs to a uniform size, thereby reducing
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
512 the number of compilations required.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
513
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
514 We do not provide a bulk inference script, but it should be straightforward to
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
515 develop on top of the `RunModel.predict` method with a parallel system for
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
516 precomputing multi-sequence alignments. Alternatively, this script can be run
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
517 repeatedly with only moderate overhead.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
518
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
519 ## Note on CASP14 reproducibility
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
520
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
521 AlphaFold's output for a small number of proteins has high inter-run variance,
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
522 and may be affected by changes in the input data. The CASP14 target T1064 is a
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
523 notable example; the large number of SARS-CoV-2-related sequences recently
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
524 deposited changes its MSA significantly. This variability is somewhat mitigated
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
525 by the model selection process; running 5 models and taking the most confident.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
526
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
527 To reproduce the results of our CASP14 system as closely as possible you must
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
528 use the same database versions we used in CASP. These may not match the default
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
529 versions downloaded by our scripts.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
530
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
531 For genetics:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
532
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
533 * UniRef90:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
534 [v2020_01](https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2020_01/uniref/)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
535 * MGnify:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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536 [v2018_12](http://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2018_12/)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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537 * Uniclust30: [v2018_08](http://wwwuser.gwdg.de/~compbiol/uniclust/2018_08/)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
538 * BFD: [only version available](https://bfd.mmseqs.com/)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
539
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
540 For templates:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
541
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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542 * PDB: (downloaded 2020-05-14)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
543 * PDB70: [2020-05-13](http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200513.tar.gz)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
544
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
545 An alternative for templates is to use the latest PDB and PDB70, but pass the
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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546 flag `--max_template_date=2020-05-14`, which restricts templates only to
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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547 structures that were available at the start of CASP14.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
548
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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549 ## Citing this work
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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550
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
551 If you use the code or data in this package, please cite:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
552
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
553 ```bibtex
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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554 @Article{AlphaFold2021,
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
555 author = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and {\v{Z}}{\'\i}dek, Augustin and Potapenko, Anna and Bridgland, Alex and Meyer, Clemens and Kohl, Simon A A and Ballard, Andrew J and Cowie, Andrew and Romera-Paredes, Bernardino and Nikolov, Stanislav and Jain, Rishub and Adler, Jonas and Back, Trevor and Petersen, Stig and Reiman, David and Clancy, Ellen and Zielinski, Michal and Steinegger, Martin and Pacholska, Michalina and Berghammer, Tamas and Bodenstein, Sebastian and Silver, David and Vinyals, Oriol and Senior, Andrew W and Kavukcuoglu, Koray and Kohli, Pushmeet and Hassabis, Demis},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
556 journal = {Nature},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
557 title = {Highly accurate protein structure prediction with {AlphaFold}},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
558 year = {2021},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
559 volume = {596},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
560 number = {7873},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
561 pages = {583--589},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
562 doi = {10.1038/s41586-021-03819-2}
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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563 }
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
564 ```
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
565
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
566 In addition, if you use the AlphaFold-Multimer mode, please cite:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
567
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
568 ```bibtex
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
569 @article {AlphaFold-Multimer2021,
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
570 author = {Evans, Richard and O{\textquoteright}Neill, Michael and Pritzel, Alexander and Antropova, Natasha and Senior, Andrew and Green, Tim and {\v{Z}}{\'\i}dek, Augustin and Bates, Russ and Blackwell, Sam and Yim, Jason and Ronneberger, Olaf and Bodenstein, Sebastian and Zielinski, Michal and Bridgland, Alex and Potapenko, Anna and Cowie, Andrew and Tunyasuvunakool, Kathryn and Jain, Rishub and Clancy, Ellen and Kohli, Pushmeet and Jumper, John and Hassabis, Demis},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
571 journal = {bioRxiv}
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
572 title = {Protein complex prediction with AlphaFold-Multimer},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
573 year = {2021},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
574 elocation-id = {2021.10.04.463034},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
575 doi = {10.1101/2021.10.04.463034},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
576 URL = {https://www.biorxiv.org/content/early/2021/10/04/2021.10.04.463034},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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577 eprint = {https://www.biorxiv.org/content/early/2021/10/04/2021.10.04.463034.full.pdf},
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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578 }
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
579 ```
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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580
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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581 ## Community contributions
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
582
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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583 Colab notebooks provided by the community (please note that these notebooks may
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
584 vary from our full AlphaFold system and we did not validate their accuracy):
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
585
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
586 * The [ColabFold AlphaFold2 notebook](https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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587 by Martin Steinegger, Sergey Ovchinnikov and Milot Mirdita, which uses an
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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588 API hosted at the Södinglab based on the MMseqs2 server [(Mirdita et al.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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589 2019, Bioinformatics)](https://academic.oup.com/bioinformatics/article/35/16/2856/5280135)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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590 for the multiple sequence alignment creation.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
591
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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592 ## Acknowledgements
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
593
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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594 AlphaFold communicates with and/or references the following separate libraries
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
595 and packages:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
596
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
597 * [Abseil](https://github.com/abseil/abseil-py)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
598 * [Biopython](https://biopython.org)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
599 * [Chex](https://github.com/deepmind/chex)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
600 * [Colab](https://research.google.com/colaboratory/)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
601 * [Docker](https://www.docker.com)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
602 * [HH Suite](https://github.com/soedinglab/hh-suite)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
603 * [HMMER Suite](http://eddylab.org/software/hmmer)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
604 * [Haiku](https://github.com/deepmind/dm-haiku)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
605 * [Immutabledict](https://github.com/corenting/immutabledict)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
606 * [JAX](https://github.com/google/jax/)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
607 * [Kalign](https://msa.sbc.su.se/cgi-bin/msa.cgi)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
608 * [matplotlib](https://matplotlib.org/)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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diff changeset
609 * [ML Collections](https://github.com/google/ml_collections)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
610 * [NumPy](https://numpy.org)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
611 * [OpenMM](https://github.com/openmm/openmm)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
612 * [OpenStructure](https://openstructure.org)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
613 * [pandas](https://pandas.pydata.org/)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
614 * [pymol3d](https://github.com/avirshup/py3dmol)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
615 * [SciPy](https://scipy.org)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
616 * [Sonnet](https://github.com/deepmind/sonnet)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
617 * [TensorFlow](https://github.com/tensorflow/tensorflow)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
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618 * [Tree](https://github.com/deepmind/tree)
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619 * [tqdm](https://github.com/tqdm/tqdm)
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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620
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621 We thank all their contributors and maintainers!
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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622
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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623 ## License and Disclaimer
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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624
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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625 This is not an officially supported Google product.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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626
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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627 Copyright 2021 DeepMind Technologies Limited.
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628
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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629 ### AlphaFold Code License
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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630
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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631 Licensed under the Apache License, Version 2.0 (the "License"); you may not use
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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632 this file except in compliance with the License. You may obtain a copy of the
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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633 License at https://www.apache.org/licenses/LICENSE-2.0.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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634
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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635 Unless required by applicable law or agreed to in writing, software distributed
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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636 under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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637 CONDITIONS OF ANY KIND, either express or implied. See the License for the
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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638 specific language governing permissions and limitations under the License.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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639
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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640 ### Model Parameters License
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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641
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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642 The AlphaFold parameters are made available for non-commercial use only, under
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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643 the terms of the Creative Commons Attribution-NonCommercial 4.0 International
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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644 (CC BY-NC 4.0) license. You can find details at:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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645 https://creativecommons.org/licenses/by-nc/4.0/legalcode
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646
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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647 ### Third-party software
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648
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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649 Use of the third-party software, libraries or code referred to in the
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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650 [Acknowledgements](#acknowledgements) section above may be governed by separate
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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651 terms and conditions or license provisions. Your use of the third-party
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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652 software, libraries or code is subject to any such terms and you should check
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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653 that you can comply with any applicable restrictions or terms and conditions
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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654 before use.
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655
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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656 ### Mirrored Databases
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657
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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658 The following databases have been mirrored by DeepMind, and are available with reference to the following:
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659
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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660 * [BFD](https://bfd.mmseqs.com/) (unmodified), by Steinegger M. and Söding J., available under a [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/).
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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661
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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662 * [BFD](https://bfd.mmseqs.com/) (modified), by Steinegger M. and Söding J., modified by DeepMind, available under a [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/). See the Methods section of the [AlphaFold proteome paper](https://www.nature.com/articles/s41586-021-03828-1) for details.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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663
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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664 * [Uniclust30: v2018_08](http://wwwuser.gwdg.de/~compbiol/uniclust/2018_08/) (unmodified), by Mirdita M. et al., available under a [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/).
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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665
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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666 * [MGnify: v2018_12](http://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/current_release/README.txt) (unmodified), by Mitchell AL et al., available free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use under [CC0 1.0 Universal (CC0 1.0) Public Domain Dedication](https://creativecommons.org/publicdomain/zero/1.0/).