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annotate alphafold.xml @ 21:e7f1b552a695 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty
author galaxy-australia
date Tue, 29 Oct 2024 02:15:36 +0000
parents 6ab1a261520a
children 3f188450ca4f
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1 <tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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2 <description> - AI-guided 3D structural prediction of proteins</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.3.2</token>
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5 <token name="@TOOL_MINOR_VERSION@">2.3</token>
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6 <token name="@VERSION_SUFFIX@">1</token>
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7 <import>macro_output.xml</import>
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8 <import>macro_test_output.xml</import>
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9 </macros>
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10 <edam_topics>
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11 <edam_topic>topic_0082</edam_topic>
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12 </edam_topics>
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13 <edam_operations>
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14 <edam_operation>operation_0474</edam_operation>
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15 </edam_operations>
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16 <xrefs>
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17 <xref type="bio.tools">alphafold_2</xref>
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18 </xrefs>
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19 <requirements>
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20 <container type="docker">neoformit/alphafold:v2.3.2_0</container>
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21 </requirements>
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22 <required_files>
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23 <include path="scripts/outputs.py" />
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24 <include path="scripts/validate_fasta.py" />
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25 <include path="scripts/alphafold.html" />
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26 </required_files>
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27 <command detect_errors="exit_code"><![CDATA[
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29 ## Developers: to test with mock alphafold run, set `export PLANEMO_TESTING=1`
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30 ## in planemo's gx_venv_n/bin/activate script. AlphaFold outputs will be copied
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31 ## from the test-data directory instead of running the tool.
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32
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33 ## $ALPHAFOLD_DB variable should point to the location containing the versioned
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34 ## AlphaFold databases - defaults to /data
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35 ## that is the directory should contain a subdir / symlink named identical as
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36 ## the value of the TOOL_MINOR_VERSION token which contains the AF reference data
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37 ## for the corresponding version
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38
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39 ## Read FASTA input -----------------------------------------------------------
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40 #if $fasta_or_text.input_mode == 'history':
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41 cp '$fasta_or_text.fasta_file' input.fasta
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42 #elif $fasta_or_text.input_mode == 'textbox':
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43 echo '$fasta_or_text.fasta_text' > input.fasta
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44 #end if
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45
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46 && python3 '$__tool_directory__/scripts/validate_fasta.py' input.fasta
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47 --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0}
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48 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0}
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49 #if $model_preset.selection == 'multimer':
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50 --multimer
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51 --max-sequences \${ALPHAFOLD_MAX_SEQUENCES:-10}
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52 #end if
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53 > alphafold.fasta
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54
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55 ## Env vars -------------------------------------------------------------------
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56 && export TF_FORCE_UNIFIED_MEMORY=1
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57 && export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0
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58 && export TODAY=`date +"%Y-%m-%d"`
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60 ## Run AlphaFold -------------------------------------------------------------
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61 #if os.environ.get('PLANEMO_TESTING'):
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62 ## Run in testing mode (mocks a successful AlphaFold run by copying outputs)
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63 && echo "Creating dummy outputs for model_preset=$model_preset.selection..."
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64 && bash '$__tool_directory__/scripts/mock_alphafold.sh' $model_preset
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65 #else:
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66 ## Run AlphaFold
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67 && python /app/alphafold/run_alphafold.py
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68 --fasta_paths alphafold.fasta
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69 --output_dir output
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70 --data_dir \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/
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71 --model_preset=$model_preset.selection
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72
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73 ## Set reference database paths
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74 --uniref90_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniref90/uniref90.fasta
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75 --mgnify_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/mgnify/mgy_clusters_2022_05.fa
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76 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_mmcif/mmcif_files
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77 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_mmcif/obsolete.dat
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78 #if $dbs == 'full':
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79 --bfd_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
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80 --uniref30_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniref30/UniRef30_2021_03
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81 #else
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82 --db_preset=reduced_dbs
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83 --small_bfd_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/small_bfd/bfd-first_non_consensus_sequences.fasta
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84 #end if
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85
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86 #if $advanced.max_template_date:
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87 --max_template_date=$advanced.max_template_date
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88 #else
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89 --max_template_date=\$TODAY
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90 #end if
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91
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92 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True}
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93
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94 #if $model_preset.selection == 'multimer':
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95 --pdb_seqres_database_path=\${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_seqres/pdb_seqres.txt
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96 --uniprot_database_path=\${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniprot/uniprot.fasta
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97 --num_multimer_predictions_per_model=$model_preset.num_multimer_predictions_per_model
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98 #else
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99 --pdb70_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb70/pdb70
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100 #end if
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101
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102 ## Galaxy-specific options --------------------------------------------
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103 ## See https://github.com/neoformit/alphafold/tree/release_2.3.2_galaxy
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104 #if $advanced.disable_amber_relax:
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105 --disable_amber_relax
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106 #end if
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107
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108 #if $advanced.limit_model_outputs:
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109 --output_models=$limit_model_outputs
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110 #end if
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111 ## End Galaxy-specific options ----------------------------------------
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112
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113 #end if
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114
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115 ## Generate additional outputs ------------------------------------------------
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116 && python3 '$__tool_directory__/scripts/outputs.py' output/alphafold
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117 $outputs.plddts
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118 $outputs.model_pkls
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119 $outputs.pae_csv
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120 $outputs.plots
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121 $outputs.plot_msa
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122
1
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123 ## HTML output
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124 && mkdir -p '${ html.files_path }'
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125 && cp output/alphafold/extra/alphafold.html '${html}'
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126 && cp output/alphafold/ranked_*.pdb '${html.files_path}'
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127
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128 ## This is a (hacky) fix for a bug that has appeared in multiple Pulsar servers.
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129 ## The working directory ends up two levels deep and the visualization html page
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130 ## fails to load the PDB files as static assets.
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131 && (([ -d working ] && cp -r working/* .) || true)
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132
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133 ]]></command>
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134 <inputs>
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135 <conditional name="fasta_or_text">
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136 <param name="input_mode" type="select" label="Fasta Input" help="Protein sequence(s) to fold. Input can be fasta file from history, or text. Sequence must be valid IUPAC amino acid characters. We recommend submitting sequences with a maximum length of 3000AA, because run time scales exponentially with sequence length. If multiple-sequence FASTA file provided, multimer mode must be selected.">
0
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137 <option value="history">Use fasta from history</option>
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138 <option value="textbox">Paste sequence into textbox</option>
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139 </param>
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140 <when value="history">
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141 <param name="fasta_file" type="data" multiple="false" format="fasta" label="Fasta file from history" help="Select single FASTA protein file from your history. If you wish to fold multiple proteins, submit an individual job for each protein. If you wish to run AlphaFold multimer, please supply multiple sequences in this file." />
0
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142 </when>
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143 <when value="textbox">
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144 <param name="fasta_text" type="text" area="true" value="" label="Paste sequence" help="Paste single protein sequence into the textbox. If you wish to fold multiple proteins, submit individual jobs for each protein. If you wish to run AlphaFold multimer, please supply multiple sequences in FASTA format." />
0
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145 </when>
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146 </conditional>
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147
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148 <param
10
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149 name="dbs"
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150 type="select"
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151 display="radio"
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152 label="Select database"
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153 help="The reduced database allows significantly faster run time in
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154 exchange for a small loss in accuracy."
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155 >
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156 <option value="reduced" selected="true">Reduced database</option>
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157 <option value="full">Full database</option>
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158 </param>
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159
20
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160 <conditional name="model_preset">
10
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161 <param
20
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162 name="selection"
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163 type="select"
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164 label="Model preset"
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165 help="Select which prediction model to run. The monomer model is the most accurate for single protein prediction. The multimer model allows prediction of protein complexes."
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166 >
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167 <option value="monomer" selected="true">monomer - default prediction model</option>
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168 <option value="monomer_ptm">
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169 monomer_ptm - slightly less accurate version of the monomer model, but provides a pairwise alignment error (PAE) matrix
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170 </option>
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171 <option value="multimer">
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172 multimer - model a protein complex (requires multi-sequence FASTA input)
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173 </option>
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174 </param>
20
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175 <when value="monomer"></when>
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176 <when value="monomer_ptm"></when>
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177 <when value="multimer">
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178 <param
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179 name="num_multimer_predictions_per_model"
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galaxy-australia
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180 type="integer"
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181 value="5"
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galaxy-australia
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182 label="Multimer predictions per model"
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183 help="How many predictions (each with a different random seed) will be generated per model. E.g. if this is 2 and there are 5 models then there will be 10 predictions per input. For a small drop in accuracy you may wish to run a single seed per model (default 5, max 10)."
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184 min="1"
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185 max="10"
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186 />
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187 </when>
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188 </conditional>
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189
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190 <section name="advanced" title="Advanced options" expanded="false">
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galaxy-australia
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191 <param
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galaxy-australia
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192 name="max_template_date"
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193 type="text"
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194 label="Max template date (yyyy-mm-dd) (optional)"
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galaxy-australia
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195 help="The model will reference PDB structures deposited before this date only. Defaults to today's date."
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196 optional="true"
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197 >
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galaxy-australia
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198 <sanitizer>
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galaxy-australia
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199 <valid initial="string.digits">
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200 <add value="-" />
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201 </valid>
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galaxy-australia
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202 </sanitizer>
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203 <validator type="regex">[0-9]{4}-[0-9]{2}-[0-9]{2}</validator>
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204 </param>
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galaxy-australia
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205
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
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206 <param
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207 name="disable_amber_relax"
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galaxy-australia
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208 type="boolean"
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galaxy-australia
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209 label="Disable Amber relaxation"
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galaxy-australia
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210 value="false"
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galaxy-australia
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211 optional="true"
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212 help="Amber relaxation can be disabled to speed up processing time. Amber relaxation is used to refine predicted structures by removing stereochemical violations, resulting in more accurate prediction of side-chain geometry. Disabling this option with large proteins may lead to artefacts in the predicted structure. Disabling amber relax will result in the unrelaxed models being collected as PDB outputs."
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
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213 />
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214
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
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diff changeset
215 <param
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
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216 name="limit_model_outputs"
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galaxy-australia
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217 type="integer"
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galaxy-australia
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218 label="Limit model outputs"
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galaxy-australia
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219 value="5"
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220 help="Limit the number of models to output. The top N models will be output, where N is the value entered here (default 5). Please note that the top-ranking model is not always the correct one, and it is usually recommended to inspect multiple models. Reducing the number of models will result in a slight reduction in run time."
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galaxy-australia
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221 min="1"
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222 max="5"
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223 />
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
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224 </section>
9
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225
14
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226 <section name="outputs" title="Optional outputs" expanded="false">
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227 <param
15
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galaxy-australia
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228 name="plots"
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galaxy-australia
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229 type="boolean"
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230 checked="false"
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galaxy-australia
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231 truevalue="--plot"
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galaxy-australia
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232 falsevalue=""
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
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233 label="pLDDT and PAE matrix plots (per model)"
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galaxy-australia
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234 help="A two-panel plot showing pLDDT against residue position (left) and PAE (paired-alignment error) as a heatmap image with residue numbers running along vertical and horizontal axes and color at each pixel indicating PAE value for the corresponding pair of residues. (right). PAE heatmap is only produced with monomer_ptm and multimer model presets."
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
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235 />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
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diff changeset
236 <param
21
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galaxy-australia
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diff changeset
237 name="plot_msa"
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galaxy-australia
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diff changeset
238 type="boolean"
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galaxy-australia
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239 checked="false"
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galaxy-australia
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240 truevalue="--plot-msa"
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galaxy-australia
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241 falsevalue=""
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty
galaxy-australia
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242 label="MSA sequence coverage plot"
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galaxy-australia
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243 help="A heatmap showing sequence coverage across the multiple sequence alignment (MSA). This plot can help you understand if regions of low confidence are due to poor sequence coverage."
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty
galaxy-australia
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244 />
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty
galaxy-australia
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245 <param
14
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galaxy-australia
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diff changeset
246 name="confidence_scores"
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galaxy-australia
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diff changeset
247 type="boolean"
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galaxy-australia
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248 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
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diff changeset
249 label="Per-model confidence scores"
21
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty
galaxy-australia
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diff changeset
250 help="A tabular file showing average confidence score for each model. The monomer preset is scored in plddt, the monomer_ptm preset is scored in predicted template modelling (PTM) and the multimer preset is scored in PTM+IPTM (interface PTM)."
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
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251 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
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252 <param
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galaxy-australia
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diff changeset
253 name="plddts"
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galaxy-australia
parents: 13
diff changeset
254 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
255 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
256 label="Per-residue confidence scores"
21
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty
galaxy-australia
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257 truevalue="--confidence-scores"
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
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diff changeset
258 falsevalue=""
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
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diff changeset
259 help="Alphafold produces a pLDDT score between 0-100 for each residue in the folded models. High scores represent high confidence in placement for the residue, while low scoring residues have lower confidence. This output is a tabular file with five rows (one for each output PDB model), with each column providing a pLDDT score for a single residue."
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
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diff changeset
260 />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
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diff changeset
261 <param
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
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diff changeset
262 name="pae_csv"
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galaxy-australia
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diff changeset
263 type="boolean"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
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diff changeset
264 checked="false"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
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diff changeset
265 truevalue="--pae"
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266 falsevalue=""
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267 label="Paired-alignment error (PAE)"
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268 help="A CSV-formatted matrix for each model. Only available for monomer_ptm and multimer model presets. Predicted aligned error (PAE) gives a distance error for every pair of residues. It gives AlphaFold's estimate of position error at residue X when the predicted and true structures are aligned on residue Y. Values range from 0 - 35 Angstroms."
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269 />
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270 <param
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271 name="model_pkls"
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272 type="boolean"
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273 checked="false"
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274 truevalue="--pkl"
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275 falsevalue=""
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276 label="ranked_*.pkl"
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277 help="A pickle file containing metrics used for the assessment of the model's accuracy. These include per-residue pLDDT scores (see above), predicted TM (Template Modelling) score, which is a global superposition metric and predicted aligned error (a matrix size (number of residues) x (number of residues) where each position describes the confidence of the residue's 3D position relative to another residue in the model; can be used for the interpretation of relative positions of domains). Pickle files can be read and processed using the Python 'pickle' library (requires the jax Python library). Outputs are named respective to PDB outputs."
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278 />
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279 <param
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280 name="relax_json"
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281 type="boolean"
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282 checked="false"
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283 label="relax_metrics.json"
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284 help="A JSON-formatted text file containing relax metrics (mostly remaining violations)."
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285 />
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286 <param
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287 name="timings_json"
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288 type="boolean"
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289 checked="false"
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290 label="timings.json"
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291 help="A JSON file with timings reported for each phase of the AlphaFold run."
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292 />
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293 </section>
0
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294 </inputs>
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295
0
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296 <outputs>
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297 <expand macro="output_pdb_models" />
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298 <data name="html" format="html" label="${tool.name} on ${on_string}: Visualization" />
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299 <!-- Optional outputs -->
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300 <expand macro="output_plddts" />
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301 <expand macro="output_msa_plot" />
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302 <expand macro="output_confidence_scores" />
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303 <expand macro="output_pickles" />
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304 <expand macro="output_pae_csv" />
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305 <expand macro="output_plots" />
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306 <expand macro="output_relax_json" />
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307 <expand macro="output_timings_json" />
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308 </outputs>
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309
0
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310 <tests>
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311 <!-- Test monomer with default outputs -->
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312 <test expect_num_outputs="6">
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313 <conditional name="fasta_or_text">
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314 <param name="input_mode" value="history"/>
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315 <param name="fasta_file" value="test1.fasta"/>
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316 </conditional>
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317 <param name="model_preset|selection" value="monomer"/>
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318 <expand macro="test_output_pdb_models" />
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319 </test>
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320
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321 <!-- Test monomer with all outputs -->
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322 <test expect_num_outputs="19">
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323 <conditional name="fasta_or_text">
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324 <param name="input_mode" value="history"/>
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325 <param name="fasta_file" value="test1.fasta"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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326 </conditional>
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327 <param name="model_preset|selection" value="monomer"/>
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328 <param name="outputs|plots" value="true"/>
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329 <param name="outputs|confidence_scores" value="true"/>
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330 <param name="outputs|plddts" value="true"/>
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331 <param name="outputs|pae_csv" value="true"/>
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332 <param name="outputs|model_pkls" value="true"/>
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333 <param name="outputs|relax_json" value="true"/>
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334 <expand macro="test_output_plots_1" />
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335 <expand macro="test_output_confidence_scores" />
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336 <expand macro="test_output_plddts" />
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337 <expand macro="test_output_pdb_models" />
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338 <expand macro="test_output_pickles" />
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339 <expand macro="test_output_relax_json" />
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340 </test>
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341
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342 <!-- Test monomer_ptm with all outputs -->
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
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343 <test expect_num_outputs="24">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
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344 <conditional name="fasta_or_text">
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345 <param name="input_mode" value="history"/>
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346 <param name="fasta_file" value="test1.fasta"/>
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347 </conditional>
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348 <param name="model_preset|selection" value="monomer_ptm"/>
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349 <param name="outputs|plots" value="true"/>
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350 <param name="outputs|confidence_scores" value="true"/>
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351 <param name="outputs|plddts" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
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352 <param name="outputs|pae_csv" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
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353 <param name="outputs|model_pkls" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
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354 <param name="outputs|relax_json" value="true"/>
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355 <expand macro="test_output_plots_2" />
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356 <expand macro="test_output_confidence_scores" />
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357 <expand macro="test_output_plddts" />
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358 <expand macro="test_output_pdb_models" />
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359 <expand macro="test_output_pickles" />
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360 <expand macro="test_output_relax_json" />
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361 <expand macro="test_output_pae_csv" />
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362 </test>
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363
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364 <!-- Test multimer with all outputs -->
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365 <test expect_num_outputs="24">
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366 <conditional name="fasta_or_text">
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367 <param name="input_mode" value="history"/>
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368 <param name="fasta_file" value="multimer.fasta"/>
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369 </conditional>
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370 <param name="model_preset|selection" value="multimer"/>
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371 <param name="outputs|plots" value="true"/>
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372 <param name="outputs|confidence_scores" value="true"/>
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373 <param name="outputs|plddts" value="true"/>
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374 <param name="outputs|pae_csv" value="true"/>
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375 <param name="outputs|model_pkls" value="true"/>
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376 <param name="outputs|relax_json" value="true"/>
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377 <param name="outputs|timings_json" value="true"/>
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378 <expand macro="test_output_plots_3" />
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379 <expand macro="test_output_confidence_scores" />
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380 <expand macro="test_output_plddts" />
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381 <expand macro="test_output_pdb_models" />
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382 <expand macro="test_output_pickles" />
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383 <expand macro="test_output_relax_json" />
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384 <expand macro="test_output_timings_json" />
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385 <expand macro="test_output_pae_csv" />
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386 </test>
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387 </tests>
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388 <help><![CDATA[
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389
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390 .. class:: infomark
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391
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392 | AlphaFold v2: AI-guided 3D structural prediction of proteins
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393 |
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394 | **NOTE: this tool packages** `a modified branch of AlphaFold v2.3.2. <https://github.com/neoformit/alphafold/tree/release_2.3.2_galaxy>`_
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395 |
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396 | This means that the neural network has been trained on PDBs with a release
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397 | date before 2021-09-30 (the training cutoff was 2018-04-30 until ``v2.3.0``).
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398 |
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399 | Find out more in the technical and release notes:
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400 |
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401
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402 - `Release notes for v2.3.2 <https://github.com/deepmind/alphafold/releases/tag/v2.3.2>`_
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403 - `Technical notes for v2.3 <https://github.com/deepmind/alphafold/blob/main/docs/technical_note_v2.3.0.md>`_
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404
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405 **What it does**
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406
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407 *What is AlphaFold?*
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408
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409 | AlphaFold is a program which uses neural networks to predict the tertiary (3D) structure of proteins. AlphaFold accepts an amino acid sequence in Fasta format, which will be "folded" into a 3D model.
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410 |
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411
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412 *What makes AlphaFold different?*
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413
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414 | The ability to use computers to predict 3D protein structures with high accuracy is desirable because it removes the time-consuming and costly process of determining structures experimentally.
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415 | In-silico protein folding has been an active field of research for decades, but existing tools were slower and far less reliable than AlphaFold.
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416 | AlphaFold represents a leap forward by regularly predicting structures to atomic-level accuracy, even when no similar structures are known.
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417 |
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418
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419
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420 **Input**
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421
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422 *Amino acid sequence*
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423
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424 | AlphaFold monomer (default) accepts a **single amino acid sequence** in FASTA format.
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425 | You can choose to input either a file from your Galaxy history or paste a sequence into a text box.
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426 | If you choose the ``multimer`` option, you can supply a FASTA file containing **multiple sequences** to be folded concurrently into a multimer.
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427 |
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428 | For pairwise screening of target-candidate with multimer, you can submit a list of paired protein sequences in batch mode (i.e. two protein sequences in each FASTA file).
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429 |
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430
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431 **Outputs**
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432
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433 *Visualization*
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434
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435 An interactive 3D graphic of the best predicted molecular structures.
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436 This output can be opened in Galaxy to give a visual impression of the results, with different structural representations to choose from.
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437 Open the "Visualization" history output by clicking on the "view data" icon:
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438
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439 .. image:: https://github.com/usegalaxy-au/galaxy-local-tools/blob/1a8d3e8daa7ccc5a345ca377697735ab95ed0666/tools/alphafold/static/img/alphafold-visualization.png?raw=true
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440 :height: 520
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441 :alt: Result visualization
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442
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443 |
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444
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445 *PDB files*
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446
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447 | PDB (Protein Data Bank) files (5 by default) are be created, ordered by rank, as predicted by AlphaFold. The tool produces 5 models by default, but this can be reduced with the "Limit model outputs" for a reduced run time.
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448 | These files describe the molecular structures and can be used for downstream analysis. e.g. *in silico* molecular docking.
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449 | **PLEASE NOTE** that all outputs have been renamed to their respective rank order, including model and model.pkl files.
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450 |
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451
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452 *Model confidence scores (optional)*
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453
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454 | This optional output produces a file which describes the confidence scores for each model (based on `pLDDTs <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799472/>`_, or the ``iptm+ptm`` score if run in multimer mode) which may be useful for downstream analysis.
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455 | Model confidence scores are also included as a column (replacing ``bFactor``) in the default PDB output.
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456 |
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457 |
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458
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459 *Model data files (ranked_n.pkl)*
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460
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461 | Per-model data stored in pickle files (a Python binary data format). These files can be used as inputs to downstream analysis software (such as Chimera X) for visualizing structures and computing kinetics between protein multimers and domains.
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462 | The tool will produce one ``.pkl`` output for each PDB model.
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463 |
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464 |
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465
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466 *pLDDT + PAE plots (optional)*
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468 | A two-panel figure in PNG format showing:
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469 | a) pLDDT score plotted against residue position
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470 | b) a heatmap of predicted-alignment error (PAE) with residue position running along vertical and horizontal axes and color at each pixel indicating PAE value for the corresponding pair of residues.
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471 | Panel b) is only produced for ``monomer_ptm`` and ``multimer`` model presets.
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472 |
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473 |
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474
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475 *MSA sequence coverage plot (optional)*
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476
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477 | A heatmap in PNG format showing:
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478 | a) Per-position sequence identity to query as a heatmap
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479 | b) Per-position sequence coverage as a line plot
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480 |
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481 | This plot can help you understand if regions of low confidence are due to poor sequence coverage, rather than
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482 | limitations of the model or intrinsically unstable regions.
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483 |
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484 |
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485
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486 *Model predicted-alignment error matrix (pae_ranked_n.csv)*
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487
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488 | Per-model predicted-alignment error (PAE) matrix - only available with the ``monomer_ptm`` and ``multimer`` model presets.
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489 | The tool will produce one ``.csv`` output for each PDB model.
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490 |
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491 |
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492
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493 *relax_metrics.json (optional)*
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494
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495 | A JSON-formatted text file containing relax metrics (primarily remaining violations).
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496 |
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497 |
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498
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499 *timings.json (optional)*
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500
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501 | A JSON-formatted text file containing the timings for each phase of the prediction.
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502 |
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503 |
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504
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505 **AlphaFold configuration**
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506
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507 | We have configured AlphaFold to run with the parameters suggested by default on `AlphaFold's GitHub <https://github.com/deepmind/alphafold>`_.
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508 | This means that it runs with Amber relaxation enabled, with relaxed PDB models collected as output datasets (ranked\_*.pdb files). If there are additonal parameters that you would like to interact with, please `send a support request to Galaxy AU <https://site.usegalaxy.org.au/request/support>`_, or open an issue on `our GitHub <https://github.com/usegalaxy-au/tools-au>`_.
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509 |
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510 |
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511
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512 **External Resources**
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513
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514 We highly recommend checking out the
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515 `Alphafold Protein Structure Database <https://alphafold.ebi.ac.uk/>`_,
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516 which contains pre-computed structures for over 200 million known proteins.
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517 See also:
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518
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519 - `Google Deepmind's article on AlphaFold <https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology>`_
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520 - `AlphaFold source code on GitHub <https://github.com/deepmind/alphafold>`_
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521
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522 *Downstream analysis*
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523
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524 | Obtaining a protein structure prediction is the first step in many analyses.
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525 | The 3D models created by AlphaFold can be used in downstream analysis, including the following:
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526 |
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527
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528 - Inspecting protein features
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529 3D viewers (pymol, chimera, ngl, blender) can be used to inspect active sites, regulatory domains, binding sites.
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530 - Molecular docking
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531 3D structures can be used to predict the binding affinity of different compounds.
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532 This is especially useful in screening drug candidates.
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533 - Protein-protein interactions
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534 Proteins associate in many biological processes, including intracellular signalling pathways and protein complex formation.
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535 To predict these interactions, other programs may ingest 3D models predicted by AlphaFold. Proprietary softwares include `GOLD <https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/>`_ and `SeeSAR <https://www.biosolveit.de/SeeSAR>`_, but many `free and open-source options <https://en.wikipedia.org/wiki/List_of_protein-ligand_docking_software>`_ are available such as `AutoDock <https://autodock.scripps.edu/>`_, `SwissDock <http://www.swissdock.ch/>`_, `DockQ <https://github.com/bjornwallner/DockQ>`_, `MM-Align <https://zhanggroup.org/MM-align/>`_ and `TM-Align <https://zhanggroup.org/TM-align/>`_. Protein-protein interactions are often inferred from AlphaFold-Multimer predictions, which provide a level of confidence in binding affinity between homomer/heteromer subunits.
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536
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537 ]]></help>
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538 <citations>
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539 <citation type="doi">https://doi.org/10.1038/s41586-021-03819-2</citation>
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540 <citation type="doi">https://doi.org/10.1101/2021.10.04.463034</citation>
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541 </citations>
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542 </tool>