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annotate alphafold.xml @ 0:7ae9d78b06f5 draft

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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
author galaxy-australia
date Fri, 28 Jan 2022 04:56:29 +0000
parents
children 6c92e000d684
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1 <tool id="alphafold" name="alphafold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>Alphafold v2.0: AI-guided 3D structure prediction of proteins</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.0.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <edam_topics>
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8 <edam_topic>topic_0082</edam_topic>
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9 </edam_topics>
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10 <edam_operations>
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11 <edam_operation>operation_0474</edam_operation>
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12 </edam_operations>
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13 <requirements>
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14 <container type="docker">neoformit/alphafold-galaxy@sha256:6adf7f07062b307d08c11130c39a28abc7c290b23f6c347b09c2c649c054c338</container>
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15 </requirements>
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16 <command detect_errors="exit_code"><![CDATA[
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17 ## fasta setup ----------------------------
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18 #if $fasta_or_text.input_mode == 'history':
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19 cp '$fasta_or_text.fasta_file' input.fasta &&
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20
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21 #elif $fasta_or_text.input_mode == 'textbox':
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22 echo '$fasta_or_text.fasta_text' > input.fasta &&
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23 #end if
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24
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25 python3 '$__tool_directory__/validate_fasta.py' input.fasta &&
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26
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27 ## env vars -------------------------------
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28 export TF_FORCE_UNIFIED_MEMORY=1 &&
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29 export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 &&
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30 export DATE=`date +"%Y-%m-%d"` &&
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31
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32 ## run alphafold -------------------------
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33 ln -s /app/alphafold/alphafold alphafold &&
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34 python /app/alphafold/run_alphafold.py
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35 --fasta_paths alphafold.fasta
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36 --output_dir output
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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37 --data_dir /data ## location of the alphafold databases on pulsar node --> could this maybe a env var? $ALPHAFOLD_DB --> \${ALPHAFOLD_DB:-/data}
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38 --uniref90_database_path /data/uniref90/uniref90.fasta
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39 --mgnify_database_path /data/mgnify/mgy_clusters_2018_12.fa
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40 --pdb70_database_path /data/pdb70/pdb70
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41 --template_mmcif_dir /data/pdb_mmcif/mmcif_files
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42 --obsolete_pdbs_path /data/pdb_mmcif/obsolete.dat
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43 --max_template_date=\$DATE
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44 --bfd_database_path /data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
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45 --uniclust30_database_path /data/uniclust30/uniclust30_2018_08/uniclust30_2018_08
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46 &&
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47
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48 ## for dry run testing
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49 ## cp -r '$__tool_directory__/output' . &&
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50
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51 ## generate extra outputs -----------------
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52 ## plddts
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53 python3 '$__tool_directory__/gen_extra_outputs.py' output/alphafold $output_plddts &&
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54
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55 ## html
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56 mkdir -p '${ html.files_path }' &&
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57 cp '$__tool_directory__/alphafold.html' ${html} &&
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58 cp output/alphafold/ranked_*.pdb '${html.files_path}' &&
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59
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60 ## For some reason the working directory ends up being one level too deep!
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61 mv working/* .
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62 ]]></command>
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63 <inputs>
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64 <conditional name="fasta_or_text">
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65 <param name="input_mode" type="select" label="Fasta Input" help="Single protein sequence to fold. Input can be fasta file from history, or text. Provide only 1 sequence per job.">
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66 <option value="history">Use fasta from history</option>
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67 <option value="textbox">Paste sequence into textbox</option>
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68 </param>
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69 <when value="history">
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70 <param name="fasta_file" type="data" format="fasta" label="Fasta file from history" help="Select single fasta protein sequence from your history. If you wish to fold multiple proteins, submit an individual job for each protein." />
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71 </when>
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72 <when value="textbox">
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73 <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." />
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74 </when>
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75 </conditional>
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76 <param name="output_plddts" type="boolean" checked="false" label="Output per-residue confidence scores" truevalue="--plddts" falsevalue="" 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. Sections of low confidence often occur in disordered regions. " />
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77 </inputs>
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78 <outputs>
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79 <data name="model5" format="pdb" from_work_dir="output/alphafold/ranked_4.pdb" label="${tool.name} on ${on_string}: Model 5"/>
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80 <data name="model4" format="pdb" from_work_dir="output/alphafold/ranked_3.pdb" label="${tool.name} on ${on_string}: Model 4"/>
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81 <data name="model3" format="pdb" from_work_dir="output/alphafold/ranked_2.pdb" label="${tool.name} on ${on_string}: Model 3"/>
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82 <data name="model2" format="pdb" from_work_dir="output/alphafold/ranked_1.pdb" label="${tool.name} on ${on_string}: Model 2"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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83 <data name="model1" format="pdb" from_work_dir="output/alphafold/ranked_0.pdb" label="${tool.name} on ${on_string}: Model 1"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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84 <data name="confidence_scores" format="tsv" from_work_dir="output/alphafold/model_confidence_scores.tsv" label="${tool.name} on ${on_string}: Model confidence scores"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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85 <data name="plddts" format="tsv" from_work_dir="output/alphafold/plddts.tsv" label="${tool.name} on ${on_string}: Per-residue confidence scores (plddts)">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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86 <filter>(output_plddts)</filter>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
87 </data>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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88 <data name="html" format="html" label="${tool.name} on ${on_string}: Visualization" />
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
89 </outputs>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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90 <tests>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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91 <test expect_num_outputs="8">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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92 <conditional name="fasta_or_text">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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93 <param name="input_mode" value="history"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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94 <param name="fasta_file" value="test1.fasta"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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95 </conditional>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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96 <param name="output_plddts" value="true"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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97 <output name="plddts">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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98 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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99 <has_n_columns n="2"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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100 <has_n_lines n="6"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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101 <has_size value="2900" delta="300"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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102 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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103 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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104 <output name="confidence_scores">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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105 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
106 <has_n_columns n="2"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
107 <has_n_lines n="6"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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108 <has_size value="70" delta="50"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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109 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
110 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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111 <output name="model1">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
112 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
113 <has_n_columns n="12"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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114 <has_n_lines n="1517"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
115 <has_size value="123000" delta="10000"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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116 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
117 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
118 <output name="model2">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
119 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
120 <has_n_columns n="12"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
121 <has_n_lines n="1517"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
122 <has_size value="123000" delta="10000"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
123 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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124 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
125 <output name="model3">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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diff changeset
126 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
127 <has_n_columns n="12"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
128 <has_n_lines n="1517"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
129 <has_size value="123000" delta="10000"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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diff changeset
130 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
131 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
132 <output name="model4">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
133 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
134 <has_n_columns n="12"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
135 <has_n_lines n="1517"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
136 <has_size value="123000" delta="10000"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
137 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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diff changeset
138 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
139 <output name="model5">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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diff changeset
140 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
141 <has_n_columns n="12"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
142 <has_n_lines n="1517"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
143 <has_size value="123000" delta="10000"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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diff changeset
144 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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145 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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146 </test>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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147 </tests>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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148 <help><![CDATA[
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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149
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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150 .. class:: infomark
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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151
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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152 **What it does**
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153
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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154 | AlphaFold v2.0: AI-guided 3D structure prediction of proteins
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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155 |
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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156
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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157 *What is AlphaFold?*
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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158
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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159 | 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), then will 'fold' that sequence into a 3D model.
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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160 | NOTE: AlphaFold has a number of versions - this tool uses AlphaFold v2.0.
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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161 |
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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162
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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163 *What makes AlphaFold different?*
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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164
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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165 | 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.
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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166 | In-silico protein folding has been an active field of research for decades, but existing tools ran more slowly and with less reliability than AlphaFold.
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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167 | AlphaFold represents a leap forward by regularly predicting structures to atomic-level accuracy, even when no similar structures are known.
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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168 |
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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169
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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170 *Downstream analysis*
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171
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172 | Obtaining a protein fold is the first step in many analyses.
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173 | The 3D models created by AlphaFold can be used in downstream analysis, including the following:
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174 |
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175
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176 - Inspecting protein features
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177 3D viewers (pymol, chimera, ngl, blender) can be used to inspect active sites, regulatory domains, binding sites.
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178 - Molecular docking
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179 3D structures can be used to predict the binding affinity of different compounds.
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180 This is especially useful in screening drug candidates.
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181 - Protein-protein interactions
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182 Proteins associate in many biological processes, including intracellular signalling pathways and protein complex formation.
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183 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/>`_ and `SwissDock <http://www.swissdock.ch/>`_.
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184
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185 *Expected run times*
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186
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187 .. image:: https://github.com/usegalaxy-au/galaxy-local-tools/blob/1a8d3e8daa7ccc5a345ca377697735ab95ed0666/tools/alphafold/static/img/alphafold_runtime_graph.png?raw=true
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188 :height: 520
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189 :alt: Run time graph
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190
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191 |
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192 | In general, we observe a quadratic relationship between sequence length and time to fold.
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193 | Once your job begins, a sequence of 50aa will take approximately 1hr to complete, while a sequence of 2000aa will take about 18hrs.
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194 |
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195
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196 **Input**
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197
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198 *Amino acid sequence*
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199
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200 | AlphaFold accepts a **single amino acid sequence** in FASTA format.
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201 | You can choose to input either a file from your Galaxy history or paste a sequence into a text box.
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202 | Please paste only a single sequence - we can only process a single sequence per job.
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203 | Multiple sequences will return an error.
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204 |
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205
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206 **Outputs**
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207
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208 *Visualization*
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209
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210 | An interactive 3D graphic of the best predicted molecular structures.
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211 | 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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212 | Open the "Visualization" history output by clicking on the "view data" icon:
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213 |
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214
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215 .. image:: https://github.com/usegalaxy-au/galaxy-local-tools/blob/1a8d3e8daa7ccc5a345ca377697735ab95ed0666/tools/alphafold/static/img/alphafold-visualization.png?raw=true
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216 :height: 520
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217 :alt: Result visualization
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218
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219 |
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220
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221 *PDB files*
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222
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223 | Five PDB (Protein Data Bank) files will be created for the best ranking models predicted by AlphaFold.
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224 | These files describe the molecular structures and can be used for downstream analysis. e.g. *in silico* molecular docking.
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225 |
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226
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227 *Model confidence scores (optional)*
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228
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229 | 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/>`_) which may be useful for downstream analysis.
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230 | Model confidence scores are also included as a column in the default PDB output.
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231 |
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232
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233 **External Resources**
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234
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235 We recommend checking out the
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236 `Alphafold Protein Structure Database <https://alphafold.ebi.ac.uk/>`_,
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237 which contains predicted sequences for thousands of Human proteins. See also:
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238
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239 - `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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240 - `AlphaFold source code on GitHub <https://github.com/deepmind/alphafold>`_
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241
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242 ]]></help>
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243 <citations>
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244 <citation type="doi">https://doi.org/10.1038/s41586-021-03819-2</citation>
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245 </citations>
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246 </tool>