Protein-Quest: Finding structural treasures in the protein jungle

Protein-Quest: Finding structural treasures in the protein jungle A.L. Engel1, S.Verhoeven2, A.M.J.J. Bonvin1 2. Netherlands eScience center 1. Faculty of Science - Chemistry, Bijvoet Center, Utrecht University (The Netherlands) Greetings, Adventurer. I am in need of a protein dataset to train my machine learning model. However, I lack the time to search through the dense protein forest down the road. Please help me find the perfect proteins that meet my training needs. [email protected] Use the Protein-Quest search function to retrieve a list of UniProt IDs fitting your criteria. Provide different parameters such as subcellular location, molecular function, and minimum/maximum sequence length. Then use Protein-Quest search to list PDB and AlphaFold structures based on the UniProt list. If needed, use the search function to also retrieve a list of interaction partners, complexes it is is present in, EMDB IDs and further details from UniProt. UniProt AlphaFold PDB AlphaFold UniProt PDB Discard Use Protein-Quest filter to clean up the collected structure files. Remove residues from AlphaFold structures below a chosen confidence threshold (pLDDT) from the structure file and then re-filter based on structure size. Split the structure files from the PDB and AlphaFold into their individual chains and filter out structures based on their ratio of secondary structure elements. Lastly, use Protein-Quest convert to convert the structure files to the format that is required for your specific usage. Optionally, generate a final list of UniProt IDs containing IDs left after completing the Protein-Quest filter objective. If you are stuck during any of the quest objectives, please see the quest log or the Protein-Quest walkthrough. https://github.com/haddocking/protein-quest After completing the first objective, use the Protein-Quest retrieve function to collect all the structure files. If you have collected a list of EMDB IDs, then also retrieve the corresponding EM density maps. protein-quest search uniprot \ --taxon-id 9606 \ --subcellular-location-go GO:0005634 \ --molecular-function-go GO:0003677 \ uniprot_accs.txt protein-quest retrieve alphafold alphafold.csv downloads-af/ protein-quest filter secondary-structure \ --ratio-min-helix-residues 0.5 \ --write-stats filtered-ss/stats.csv \ ./filtered-chains ./filtered-ss protein-quest convert uniprot ./filtered-ss \ uniprot_accs.filtered.txt pLDDT < 70 ? Quest Log Walkthrough Keep