{"paper":{"title":"Applications of Knot Theory for the Improvement of the AlphaFold Protein Database","arxiv_id":"2412.11229","primary_cat":"q-bio.BM","submitted_at":"2024-12-15T15:52:05+00:00","version_compiled":"v1"},"notice":"Every quoted sentence is the authors' text from the arXiv listing abstract. Labels and probabilities are the outputs of classifier-1.13.0 on the question bank abstract-p1-20260923, exactly as returned. No sentence in this record was written by a language model.","schema":"pith.compiled-record/v0","status":"compiled","abstract":{"source":"arXiv listing abstract v1","sentences":[{"i":0,"p":1.0,"id":"s0","own":false,"role":"background","text":"AlphaFold, a groundbreaking protein prediction model, has revolutionized protein structure prediction, populating the AlphaFold Protein Database (AFDB) with millions of predicted structures.","hedge":{"p":1.0,"label":"asserted"},"own_p":0.05,"main_claim_p":0.02,"quantitative":false,"quantitative_p":0.4,"role_probabilities":{"gap":0.0,"method":0.0,"result":0.0,"background":1.0,"limitation":0.0,"future_work":0.0,"contribution":0.0,"interpretation":0.0}},{"i":1,"p":0.73,"id":"s1","own":false,"role":"gap","text":"However, AlphaFold's accuracy in predicting proteins with intricate topologies, such as knots, remains a concern.","hedge":{"p":0.83,"label":"asserted"},"own_p":0.05,"main_claim_p":0.04,"quantitative":false,"quantitative_p":0.04,"role_probabilities":{"gap":0.73,"method":0.0,"result":0.0,"background":0.24,"limitation":0.03,"future_work":0.0,"contribution":0.0,"interpretation":0.0}},{"i":2,"p":0.98,"id":"s2","own":true,"role":"contribution","text":"This study investigates AlphaFold's performance in predicting knotted proteins and explores potential solutions to enhance the AFDB's reliability.","hedge":{"p":0.77,"label":"asserted"},"own_p":0.58,"main_claim_p":0.04,"quantitative":false,"quantitative_p":0.03,"role_probabilities":{"gap":0.01,"method":0.0,"result":0.0,"background":0.01,"limitation":0.0,"future_work":0.0,"contribution":0.98,"interpretation":0.0}},{"i":3,"p":0.95,"id":"s3","own":true,"role":"method","text":"Forty-five experimentally verified knotted protein structures from the KnotProt database were compared to their AlphaFold-generated counterparts.","hedge":{"p":0.99,"label":"asserted"},"own_p":0.9,"main_claim_p":0.02,"quantitative":true,"quantitative_p":0.96,"role_probabilities":{"gap":0.0,"method":0.95,"result":0.0,"background":0.0,"limitation":0.0,"future_work":0.0,"contribution":0.05,"interpretation":0.0}},{"i":4,"p":1.0,"id":"s4","own":true,"role":"method","text":"Knot analysis was performed using PyKnot, a PyMOL plugin, employing both Gauss codes and Alexander-Briggs knot notations.","hedge":{"p":0.99,"label":"asserted"},"own_p":0.87,"main_claim_p":0.02,"quantitative":false,"quantitative_p":0.17,"role_probabilities":{"gap":0.0,"method":1.0,"result":0.0,"background":0.0,"limitation":0.0,"future_work":0.0,"contribution":0.0,"interpretation":0.0}},{"i":5,"p":1.0,"id":"s5","own":true,"role":"result","text":"Results showed 95.6% accuracy in predicting the general shape of knots using Alexander-Briggs notation.","hedge":{"p":1.0,"label":"asserted"},"own_p":0.89,"main_claim_p":0.1,"quantitative":true,"quantitative_p":0.99,"role_probabilities":{"gap":0.0,"method":0.0,"result":1.0,"background":0.0,"limitation":0.0,"future_work":0.0,"contribution":0.0,"interpretation":0.0}},{"i":6,"p":0.82,"id":"s6","own":true,"role":"result","text":"However, Gauss code analysis revealed a 55.6% discrepancy, indicating AlphaFold's limitations in accurately representing the intricate orientation and directionality of knots.","hedge":{"p":0.52,"label":"hedged_possibility"},"own_p":0.93,"main_claim_p":0.23,"quantitative":true,"quantitative_p":0.99,"role_probabilities":{"gap":0.0,"method":0.0,"result":0.82,"background":0.0,"limitation":0.0,"future_work":0.0,"contribution":0.0,"interpretation":0.18}},{"i":7,"p":0.97,"id":"s7","own":true,"role":"interpretation","text":"This Applications of Knot Theory for the improvement of the AlphaFold Protein Database suggests potential inaccuracies in a significant portion of the AFDB's knotted protein structures.","hedge":{"p":1.0,"label":"hedged_possibility"},"own_p":0.69,"main_claim_p":0.75,"quantitative":false,"quantitative_p":0.09,"role_probabilities":{"gap":0.0,"method":0.0,"result":0.02,"background":0.0,"limitation":0.0,"future_work":0.0,"contribution":0.01,"interpretation":0.97}},{"i":8,"p":0.98,"id":"s8","own":true,"role":"future_work","text":"The study underscores the need for improved knot representation in AlphaFold and proposes potential solutions, including transitioning to a single-module design or removing incorrectly predicted structures from the AFDB.","hedge":{"p":0.59,"label":"asserted"},"own_p":0.64,"main_claim_p":0.32,"quantitative":false,"quantitative_p":0.04,"role_probabilities":{"gap":0.0,"method":0.0,"result":0.0,"background":0.0,"limitation":0.0,"future_work":0.98,"contribution":0.01,"interpretation":0.01}},{"i":9,"p":0.7,"id":"s9","own":false,"role":"interpretation","text":"These findings highlight the importance of 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