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Title: GitHub - PombertLab/3DFI: The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.

Open Graph Title: GitHub - PombertLab/3DFI: The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.

X Title: GitHub - PombertLab/3DFI: The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.

Description: The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space. - PombertLab/3DFI

Open Graph Description: The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space. - PombertLab/3DFI

X Description: The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space. - PombertLab/3DFI

Opengraph URL: https://github.com/PombertLab/3DFI

X: @github

direct link

Domain: patch-diff.githubusercontent.com

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Exampleshttps://patch-diff.githubusercontent.com/PombertLab/3DFI/tree/master/Examples
Homology_searchhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/tree/master/Homology_search
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Predictionhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/tree/master/Prediction
Predictionhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/tree/master/Prediction
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README.mdhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/blob/master/README.md
create_3DFI_db.plhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/blob/master/create_3DFI_db.pl
create_3DFI_db.plhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/blob/master/create_3DFI_db.pl
run_3DFI.plhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/blob/master/run_3DFI.pl
run_3DFI.plhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/blob/master/run_3DFI.pl
run_visualizations.plhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/blob/master/run_visualizations.pl
run_visualizations.plhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/blob/master/run_visualizations.pl
setup_3DFI.plhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/blob/master/setup_3DFI.pl
setup_3DFI.plhttps://patch-diff.githubusercontent.com/PombertLab/3DFI/blob/master/setup_3DFI.pl
READMEhttps://patch-diff.githubusercontent.com/PombertLab/3DFI
MIT licensehttps://patch-diff.githubusercontent.com/PombertLab/3DFI
https://github.com/PombertLab/3DFI/blob/master/Images/Logo.png
RSCB PDBhttps://www.rcsb.org/
Foldseekhttps://github.com/steineggerlab/foldseek
CCP4https://www.ccp4.ac.uk/
ChimeraXhttps://www.rbvi.ucsf.edu/chimerax/download.html
https://zenodo.org/doi/10.5281/zenodo.5525018
https://patch-diff.githubusercontent.com/PombertLab/3DFI#table-of-contents
Introductionhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#introduction
Getting startedhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#getting-started
Recommended hardwarehttps://patch-diff.githubusercontent.com/PombertLab/3DFI#recommended-hardware
Software requirementshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#software-requirements
Installing 3DFIhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#installing-3DFI
Initial setuphttps://patch-diff.githubusercontent.com/PombertLab/3DFI#initial-setup
Downloading the 3DFI databaseshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#downloading-the-3DFI-databases
Using 3DFIhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#Using-3DFI
A case example - Unknown proteins from Microsporidiahttps://patch-diff.githubusercontent.com/PombertLab/3DFI#a-case-example---unknown-proteins-from-microsporidia
Interpreting the resultshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#Interpreting-the-results
The 3DFI pipeline process in detailhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#the-3DFI-ipeline-process-in-detail
Preparing FASTA fileshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#preparing-fasta-files
3D structure predictionhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#3D-structure-prediction
AlphaFold2https://patch-diff.githubusercontent.com/PombertLab/3DFI#AlphaFold2---deep-learning-based-protein-structure-modeling
RoseTTAFOLDhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#RoseTTAFOLD---deep-learning-based-protein-structure-modeling
RaptorXhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#Raptorx---template-based-protein-structure-modeling
Structural homology searcheshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#Structural-homology-searches
Downloading PDB files from RCSBhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#downloading-PDB-files-from-RCSB
Creating a list of PDB titleshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#creating-a-list-of-PDB-titles
Creating or querying a Foldseek databasehttps://patch-diff.githubusercontent.com/PombertLab/3DFI#creating-or-querying-a-Foldseek-database
Creating or querying a GESAMT databasehttps://patch-diff.githubusercontent.com/PombertLab/3DFI#creating-or-querying-a-GESAMT-database
Parsing the output of homology searcheshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#Parsing-the-output-of-homology-searches
Structural alignment and visualizationhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#Structural-alignment-and-visualization
About alignment and visualizationhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#About-alignment-and-visualization
Aligning protein structures and inspecting alignments with ChimeraXhttps://patch-diff.githubusercontent.com/PombertLab/3DFI#Aligning-protein-structures-and-inspecting-alignments-with-ChimeraX
Coloring AlphaFold2 or RoseTTAFold predictions per confidence scoreshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#Coloring-AlphaFold2-or-RoseTTAFold-predictions-per-confidence-scores
Miscellaneoushttps://patch-diff.githubusercontent.com/PombertLab/3DFI#miscellaneous
Useful scriptshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#useful-scripts
Alternate predictorshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#alternate-predictors
trRosettahttps://patch-diff.githubusercontent.com/PombertLab/3DFI#trRosetta---deep-learning-based-protein-structure-modeling
trRosetta2https://patch-diff.githubusercontent.com/PombertLab/3DFI#trRosetta2---deep-learning-based-protein-structure-modeling
Funding and acknowledgmentshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#Funding-and-acknowledgments
How to citehttps://patch-diff.githubusercontent.com/PombertLab/3DFI#how-to-cite
Referenceshttps://patch-diff.githubusercontent.com/PombertLab/3DFI#references
https://patch-diff.githubusercontent.com/PombertLab/3DFI#introduction
https://patch-diff.githubusercontent.com/PombertLab/3DFI#about-function-inferences
BLASThttps://blast.ncbi.nlm.nih.gov/Blast.cgi
DIAMONDhttps://github.com/bbuchfink/diamond
HHBLITShttps://github.com/soedinglab/hh-suite
HMMERhttp://hmmer.org/
https://patch-diff.githubusercontent.com/PombertLab/3DFI#why-structural-homologs
https://patch-diff.githubusercontent.com/PombertLab/3DFI#what-is-needed-for-structure-based-homology-searches
RCSB PDBhttps://www.rcsb.org/
CAMEOhttps://www.cameo3d.org/
Foldseekhttps://github.com/steineggerlab/foldseek
CCP4https://www.ccp4.ac.uk/
PDBeFoldhttps://www.ebi.ac.uk/msd-srv/ssm/
https://patch-diff.githubusercontent.com/PombertLab/3DFI#why-this-pipeline
SWISS-MODELhttps://swissmodel.expasy.org/
PDBeFoldhttps://www.ebi.ac.uk/msd-srv/ssm/
https://patch-diff.githubusercontent.com/PombertLab/3DFI#getting-started
https://patch-diff.githubusercontent.com/PombertLab/3DFI#recommended-hardware
AlphaFold2https://github.com/deepmind/alphafold
RoseTTAFoldhttps://github.com/RosettaCommons/RoseTTAFold
paperhttps://pubmed.ncbi.nlm.nih.gov/34282049/
AlphaFold2https://github.com/deepmind/alphafold
RoseTTAFoldhttps://github.com/RosettaCommons/RoseTTAFold
RaptorXhttp://raptorx.uchicago.edu/
AlphaFold2https://github.com/deepmind/alphafold
RoseTTAFoldhttps://github.com/RosettaCommons/RoseTTAFold
HH-suite3https://github.com/soedinglab/hh-suite
AlphaFold2https://github.com/deepmind/alphafold
3DFIhttps://github.com/PombertLab/3DFI
https://patch-diff.githubusercontent.com/PombertLab/3DFI#software-requirements
aria2https://aria2.github.io/
customizedhttps://github.com/PombertLab/alphafold
AlphaFold2https://github.com/deepmind/alphafold
Dockerhttps://www.docker.com/
RoseTTAFoldhttps://github.com/RosettaCommons/RoseTTAFold
Condahttps://docs.conda.io/en/latest/
PyRosettahttp://www.pyrosetta.org/
RaptorXhttp://raptorx.uchicago.edu/
MODELLERhttps://salilab.org/modeller/
Foldseekhttps://github.com/steineggerlab/foldseek
CCP4https://www.ccp4.ac.uk/
ChimeraXhttps://www.cgl.ucsf.edu/chimerax/download.html
Perl5https://www.perl.org/
PerlIO::gziphttps://metacpan.org/pod/PerlIO::gzip
https://patch-diff.githubusercontent.com/PombertLab/3DFI#aria2
https://patch-diff.githubusercontent.com/PombertLab/3DFI#protein-structure-prediction-tools
customizedhttps://github.com/PombertLab/alphafold
RaptorXhttp://raptorx.uchicago.edu/
RoseTTAFoldhttps://github.com/RosettaCommons/RoseTTAFold
setup_3DFI.plhttps://github.com/PombertLab/3DFI/blob/master/setup_3DFI.pl
belowhttps://github.com/PombertLab/3DFI#installing-3DFI
herehttps://github.com/PombertLab/3DFI/blob/master/Notes/Installation_notes.sh
CASP14https://predictioncenter.org/casp14/
articlehttps://www.nature.com/articles/d41586-020-03348-4
AlphaFold2https://github.com/deepmind/alphafold
RaptorXhttp://raptorx.uchicago.edu/
RoseTTAFoldhttps://github.com/RosettaCommons/RoseTTAFold
licensehttp://www.pyrosetta.org/
setup_3DFI.plhttps://github.com/PombertLab/3DFI/blob/master/setup_3DFI.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#modeller
Modellerhttps://salilab.org/modeller/
herehttps://salilab.org/modeller/registration.html
herehttps://salilab.org/modeller/download_installation.html
https://patch-diff.githubusercontent.com/PombertLab/3DFI#structural-homology-tools
https://patch-diff.githubusercontent.com/PombertLab/3DFI#foldseek
setup_3DFI.plhttps://github.com/PombertLab/3DFI/blob/master/setup_3DFI.pl
Foldseekhttps://github.com/steineggerlab/foldseek
https://patch-diff.githubusercontent.com/PombertLab/3DFI#gesamt
CCP4https://www.ccp4.ac.uk/
https://patch-diff.githubusercontent.com/PombertLab/3DFI#chimerax
ChimeraXhttps://www.cgl.ucsf.edu/chimerax/download.html
https://patch-diff.githubusercontent.com/PombertLab/3DFI#perl-modules
https://patch-diff.githubusercontent.com/PombertLab/3DFI#installing-3dfi
https://patch-diff.githubusercontent.com/PombertLab/3DFI#initial-setup
setup_3DFI.plhttps://github.com/PombertLab/3DFI/blob/master/setup_3DFI.pl
Foldseekhttps://github.com/steineggerlab/foldseek
https://patch-diff.githubusercontent.com/PombertLab/3DFI#downloading-the-3dfi-databases
create_3DFI_db.plhttps://github.com/PombertLab/3DFI/blob/master/create_3DFI_db.pl
create_3DFI_db.plhttps://github.com/PombertLab/3DFI/blob/master/create_3DFI_db.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#using-3dfi
run_3DFI.plhttps://github.com/PombertLab/3DFI/blob/master/run_3DFI.pl
RCSB PDBhttps://www.rcsb.org/
https://patch-diff.githubusercontent.com/PombertLab/3DFI#a-case-example---unknown-proteins-from-microsporidia
NIAID category B pathogenhttps://www.niaid.nih.gov/research/emerging-infectious-diseases-pathogens
sequences.fastahttps://github.com/PombertLab/3DFI/tree/master/Examples/FASTA/sequences.fasta
Encephalitozoon cuniculi GB-M1https://microsporidiadb.org/micro/app/downloads/Current_Release/EcuniculiGBM1/
InterProScanhttp://www.ebi.ac.uk/interpro/search/sequence/
https://github.com/PombertLab/3DFI/blob/master/Images/no_homology.png
RCSBhttps://www.rcsb.org/
AlphaFold2https://github.com/PombertLab/3DFI/blob/master/Prediction/AlphaFold2/af2_installation_notes.sh
RoseTTAFoldhttps://github.com/PombertLab/3DFI/blob/master/Prediction/RoseTTAFold/rfold_installation_notes.sh
RaptorXhttps://github.com/PombertLab/3DFI/blob/master/Prediction/RaptorX/raptorx_installation_notes.sh
Foldseekhttps://github.com/PombertLab/3DFI/tree/foldseek
All_GESAMT_matches_per_protein.tsvhttps://github.com/PombertLab/3DFI/blob/master/Examples/Results_3DFI/Homology/GESAMT/All_GESAMT_matches_per_protein.tsv
run_visualizations.plhttps://github.com/PombertLab/3DFI/blob/master/run_visualizations.pl
run_3DFI.plhttps://github.com/PombertLab/3DFI/blob/master/run_3DFI.pl
ChimeraXhttps://www.rbvi.ucsf.edu/chimerax/download.html
https://github.com/PombertLab/3DFI/blob/master/Images/ECU03_1140-m4_3kdf_B.png
ChimeraXhttps://www.rbvi.ucsf.edu/chimerax/download.html
https://github.com/PombertLab/3DFI/blob/master/Images/ECU03_1140-m4.png
https://patch-diff.githubusercontent.com/PombertLab/3DFI#interpreting-the-results
https://patch-diff.githubusercontent.com/PombertLab/3DFI#the-3dfi-pipeline-process-in-detail
Preparing FASTA fileshttps://github.com/PombertLab/3DFI#preparing-fasta-files
3D structure predictionhttps://github.com/PombertLab/3DFI#3D-structure-prediction
Structural homology searcheshttps://github.com/PombertLab/3DFI#structural-homology-searches
Structural alignment and visualizationhttps://github.com/PombertLab/3DFI#structural-alignment-and-visualization
https://patch-diff.githubusercontent.com/PombertLab/3DFI#preparing-fasta-files
split_Fasta.plhttps://github.com/PombertLab/3DFI/blob/master/Misc_tools/split_Fasta.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#3d-structure-prediction
https://patch-diff.githubusercontent.com/PombertLab/3DFI#alphafold2---deep-learning-based-protein-structure-modeling
alphafold.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/AlphaFold2/alphafold.pl
parse_af_results.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/AlphaFold2/parse_af_results.pl
parse_af_results.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/AlphaFold2/parse_af_results.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#rosettafold---deep-learning-based-protein-structure-modeling
rosettafold.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/RoseTTAFold/rosettafold.pl
RoseTTAFoldhttps://github.com/RosettaCommons/RoseTTAFold
parse_rf_results.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/RoseTTAFold/parse_rf_results.pl
parse_rf_results.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/RoseTTAFold/parse_rf_results.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#raptorx---template-based-protein-structure-modeling
RaptorXhttp://raptorx.uchicago.edu/
raptorx.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/RaptorX/raptorx.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#structural-homology-searches
https://patch-diff.githubusercontent.com/PombertLab/3DFI#downloading-pdb-files-from-rcsb
Protein Data Bankhttps://www.rcsb.org/
herehttps://www.wwpdb.org/ftp/pdb-ftp-sites
rsynchttps://rsync.samba.org/
update_PDB.plhttps://github.com/PombertLab/3DFI/blob/master/Homology_search/update_PDB.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#creating-a-list-of-pdb-titles
PDB_headers.plhttps://github.com/PombertLab/3DFI/blob/master/Homology_search/PDB_headers.pl
PerlIO::gziphttps://metacpan.org/pod/PerlIO::gzip
https://patch-diff.githubusercontent.com/PombertLab/3DFI#creating-or-querying-a-foldseek-database
Foldseekhttps://github.com/PombertLab/3DFI/tree/foldseek
create_3DFI_db.plhttps://github.com/PombertLab/3DFI/blob/master/create_3DFI_db.pl
run_foldseek.plhttps://github.com/PombertLab/3DFI/master/foldseek/Homology_search/run_foldseek.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#creating-or-querying-a-gesamt-database
CCP4https://www.ccp4.ac.uk/
run_GESAMT.plhttps://github.com/PombertLab/3DFI/blob/master/Homology_search/run_GESAMT.pl
run_GESAMT.plhttps://github.com/PombertLab/3DFI/blob/master/Homology_search/run_GESAMT.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#parsing-the-output-of-structural-homology-searches
PDB_headers.plhttps://github.com/PombertLab/3DFI/blob/master/Homology_search/PDB_headers.pl
descriptive_matches.plhttps://github.com/PombertLab/3DFI/blob/master/Homology_search/descriptive_matches.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#parsing-the-output-of-descriptive_matchespl-per-protein-accross-all-models-from-best-q-score-to-worst
parse_all_models_by_Q.plhttps://github.com/PombertLab/3DFI/blob/master/Homology_search/parse_all_models_by_Q.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#structural-alignment-and-visualization
https://patch-diff.githubusercontent.com/PombertLab/3DFI#about-alignment-and-visualization
ChimeraXhttps://www.rbvi.ucsf.edu/chimerax/
good resulthttps://github.com/PombertLab/3DFI/blob/master/Images/Good_Match.png
false-negativehttps://github.com/PombertLab/3DFI/blob/master/Images/Bad_Predicted_Fold.png
false-positivehttps://github.com/PombertLab/3DFI/blob/master/Images/Bad_Match.png
https://patch-diff.githubusercontent.com/PombertLab/3DFI#aligning-protein-structures-and-inspecting-alignments-with-chimerax
prepare_visualizations.plhttps://github.com/PombertLab/3DFI/blob/master/Visualization/prepare_visualizations.pl
ChimeraXhttps://www.rbvi.ucsf.edu/chimerax/
run_visualizations.plhttps://github.com/PombertLab/3DFI/blob/master/run_visualizations.pl
ChimeraXhttps://www.rbvi.ucsf.edu/chimerax/download.html
https://github.com/PombertLab/3DFI/blob/master/Images/Just_PDB.png
commandshttps://www.rbvi.ucsf.edu/chimerax/docs/user/index.html
https://github.com/PombertLab/3DFI/blob/master/Images/Just_PDB_rainbow.png
https://github.com/PombertLab/3DFI/blob/master/Images/With_Alignment.png
https://patch-diff.githubusercontent.com/PombertLab/3DFI#coloring-alphafold2-or-rosettafold-predictions-per-confidence-scores
AlphaFold2https://github.com/deepmind/alphafold
RoseTTAFoldhttps://github.com/RosettaCommons/RoseTTAFold
columnshttps://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html
AlphaFold Protein Structure Databasehttps://alphafold.ebi.ac.uk/
https://github.com/PombertLab/3DFI/blob/master/Images/bfactor.png
color byattributehttps://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute
https://github.com/PombertLab/3DFI/blob/master/Images/bfactor_key.png
keyhttps://www.cgl.ucsf.edu/chimerax/docs/user/commands/key.html
https://github.com/PombertLab/3DFI/blob/master/Images/bfactor_key_cmd.png
manualhttps://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
https://patch-diff.githubusercontent.com/PombertLab/3DFI#miscellaneous
https://patch-diff.githubusercontent.com/PombertLab/3DFI#useful-scripts
https://patch-diff.githubusercontent.com/PombertLab/3DFI#splitting-pdb-files
split_PDB.plhttps://github.com/PombertLab/3DFI/blob/master/Misc_tools/split_PDB.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#renaming-files
rename_files.plhttps://github.com/PombertLab/3DFI/blob/master/Misc_tools/rename_files.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#alternate-predictors
3DFI/predictionhttps://github.com/PombertLab/3DFI/tree/master/Prediction
https://patch-diff.githubusercontent.com/PombertLab/3DFI#trrosetta---deep-learning-based-protein-structure-modeling
trRosettahttps://github.com/gjoni/trRosetta
HH-suite3https://github.com/soedinglab/hh-suite
tensorflowhttps://www.tensorflow.org/
PyRosettahttp://www.pyrosetta.org/
Uniclusthttps://uniclust.mmseqs.com/
tensorflowhttps://www.tensorflow.org/
PyRosettahttp://www.pyrosetta.org/
trRosetta_installation_notes.shhttps://github.com/PombertLab/3DFI/blob/master/Prediction/trRosetta/trRosetta_installation_notes.sh
https://patch-diff.githubusercontent.com/PombertLab/3DFI#tensorflow-115-in-conda
https://patch-diff.githubusercontent.com/PombertLab/3DFI#running-trrosetta
trRosettahttps://github.com/gjoni/trRosetta
HHsuite3https://github.com/soedinglab/hh-suite
trRosettahttps://github.com/gjoni/trRosetta
PyRosettahttp://www.pyrosetta.org/
fasta_oneliner.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/trRosetta/fasta_oneliner.pl
run_hhblits.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/trRosetta/run_hhblits.pl
create_npz.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/trRosetta/create_npz.pl
create_pdb.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/trRosetta/create_pdb.pl
PDBeFOLDhttps://www.ebi.ac.uk/msd-srv/ssm/
sanitize_pdb.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/trRosetta/sanitize_pdb.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#trrosetta2---deep-learning-based-protein-structure-modeling
trRosetta2https://github.com/RosettaCommons/trRosetta2
trRosetta2.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/trRosetta2/trRosetta2.pl
fasta_oneliner.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/trRosetta2/fasta_oneliner.pl
trRosetta2https://github.com/RosettaCommons/trRosetta2
trRosetta2.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/trRosetta2/trRosetta2.pl
parse_tr2_results.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/trRosetta2/parse_tr2_results.pl
parse_tr2_results.plhttps://github.com/PombertLab/3DFI/blob/master/Prediction/trRosetta2/parse_tr2_results.pl
https://patch-diff.githubusercontent.com/PombertLab/3DFI#funding-and-acknowledgments
https://patch-diff.githubusercontent.com/PombertLab/3DFI#how-to-cite
https://patch-diff.githubusercontent.com/PombertLab/3DFI#if-you-use-this-pipeline-please-cite-the-3dfi-publication
3DFI: a pipeline to infer protein function using structural homologyhttps://academic.oup.com/bioinformaticsadvances/article/1/1/vbab030/6424973
https://patch-diff.githubusercontent.com/PombertLab/3DFI#please-also-cite-the-tools-used-for-protein-stucture-prediction-alphafold-rosettafold-andor-raptorx-structural-homology-searches-gesamt-and-3d-visualization-chimerax-as-needed
Highly accurate protein structure prediction with AlphaFoldhttps://pubmed.ncbi.nlm.nih.gov/34265844/
Accurate prediction of protein structures and interactions using a three-track neural networkhttps://pubmed.ncbi.nlm.nih.gov/34282049/
RaptorX: exploiting structure information for protein alignment by statistical inferencehttps://pubmed.ncbi.nlm.nih.gov/21987485/
Enhanced fold recognition using efficient short fragment clusteringhttps://pubmed.ncbi.nlm.nih.gov/27882309/
UCSF ChimeraX: Structure visualization for researchers, educators, and developershttps://www.ncbi.nlm.nih.gov/pubmed/32881101
https://patch-diff.githubusercontent.com/PombertLab/3DFI#references
RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archivehttps://pubmed.ncbi.nlm.nih.gov/33186584/
RaptorX: exploiting structure information for protein alignment by statistical inferencehttps://pubmed.ncbi.nlm.nih.gov/21987485/
Template-based protein structure modeling using the RaptorX web serverhttps://pubmed.ncbi.nlm.nih.gov/22814390/
Enhanced fold recognition using efficient short fragment clusteringhttps://pubmed.ncbi.nlm.nih.gov/27882309/
Overview of the CCP4 suite and current developmentshttps://pubmed.ncbi.nlm.nih.gov/21460441/
Improved protein structure prediction using predicted interresidue orientationshttps://pubmed.ncbi.nlm.nih.gov/31896580/
UCSF ChimeraX: Structure visualization for researchers, educators, and developershttps://www.ncbi.nlm.nih.gov/pubmed/32881101
Highly accurate protein structure prediction with AlphaFoldhttps://pubmed.ncbi.nlm.nih.gov/34265844/
Accurate prediction of protein structures and interactions using a three-track neural networkhttps://pubmed.ncbi.nlm.nih.gov/34282049/
A local superposition-free score for comparing protein structures and models using distance difference testshttps://pubmed.ncbi.nlm.nih.gov/23986568/
Foldseek: fast and accurate protein structure searchhttps://www.biorxiv.org/content/10.1101/2022.02.07.479398
MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomershttps://pubmed.ncbi.nlm.nih.gov/29726907/
3d-structure https://patch-diff.githubusercontent.com/topics/3d-structure
pdb-files https://patch-diff.githubusercontent.com/topics/pdb-files
structural-homologs https://patch-diff.githubusercontent.com/topics/structural-homologs
Readme https://patch-diff.githubusercontent.com/PombertLab/3DFI#readme-ov-file
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3DFI-v1.0.1a Latest May 27, 2022 https://patch-diff.githubusercontent.com/PombertLab/3DFI/releases/tag/1.0.1a
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