{"id":"https://openalex.org/W4414511184","doi":"https://doi.org/10.1186/s13321-025-01067-4","title":"Evaluating ligand docking methods for drugging protein\u2013protein interfaces: insights from AlphaFold2 and molecular dynamics refinement","display_name":"Evaluating ligand docking methods for drugging protein\u2013protein interfaces: insights from AlphaFold2 and molecular dynamics refinement","publication_year":2025,"publication_date":"2025-09-25","ids":{"openalex":"https://openalex.org/W4414511184","doi":"https://doi.org/10.1186/s13321-025-01067-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/40999494"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01067-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01067-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01067-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01067-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072662528","display_name":"Jordi G\u00f3mez Borrego","orcid":"https://orcid.org/0000-0003-1963-5455"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Jordi G\u00f3mez Borrego","raw_affiliation_strings":["The Systems Biology of Infection Laboratory, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Aut\u00f2noma de Barcelona, 08193, Cerdanyola del Vall\u00e8s, Spain"],"affiliations":[{"raw_affiliation_string":"The Systems Biology of Infection Laboratory, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Aut\u00f2noma de Barcelona, 08193, Cerdanyola del Vall\u00e8s, Spain","institution_ids":["https://openalex.org/I123044942"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067145798","display_name":"Marc Torrent","orcid":"https://orcid.org/0000-0001-6567-3474"},"institutions":[{"id":"https://openalex.org/I123044942","display_name":"Universitat Aut\u00f2noma de Barcelona","ror":"https://ror.org/052g8jq94","country_code":"ES","type":"education","lineage":["https://openalex.org/I123044942"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Marc Torrent Burgas","raw_affiliation_strings":["The Systems Biology of Infection Laboratory, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Aut\u00f2noma de Barcelona, 08193, Cerdanyola del Vall\u00e8s, Spain. marc.torrent@uab.cat","The Systems Biology of Infection Laboratory, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Aut\u00f2noma de Barcelona, 08193, Cerdanyola del Vall\u00e8s, Spain"],"affiliations":[{"raw_affiliation_string":"The Systems Biology of Infection Laboratory, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Aut\u00f2noma de Barcelona, 08193, Cerdanyola del Vall\u00e8s, Spain. marc.torrent@uab.cat","institution_ids":["https://openalex.org/I123044942"]},{"raw_affiliation_string":"The Systems Biology of Infection Laboratory, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Aut\u00f2noma de Barcelona, 08193, Cerdanyola del Vall\u00e8s, Spain","institution_ids":["https://openalex.org/I123044942"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5072662528"],"corresponding_institution_ids":["https://openalex.org/I123044942"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":5.6527,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.96282964,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"17","issue":"1","first_page":"144","last_page":"144"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.972100019454956,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.8511999845504761},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.722599983215332},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.5946999788284302},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.43299999833106995},{"id":"https://openalex.org/keywords/macromolecular-docking","display_name":"Macromolecular docking","score":0.3375999927520752}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8511999845504761},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.722599983215332},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6546000242233276},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.5946999788284302},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.43299999833106995},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4034999907016754},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3384000062942505},{"id":"https://openalex.org/C116887118","wikidata":"https://www.wikidata.org/wiki/Q836685","display_name":"Macromolecular docking","level":3,"score":0.3375999927520752},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33219999074935913},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.295199990272522},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.2849000096321106},{"id":"https://openalex.org/C2989255885","wikidata":"https://www.wikidata.org/wiki/Q500256","display_name":"Molecular conformation","level":3,"score":0.25380000472068787},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.2522999942302704}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13321-025-01067-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01067-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01067-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:40999494","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40999494","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:410adcc038084d3d9c1593dffce64ab4","is_oa":true,"landing_page_url":"https://doaj.org/article/410adcc038084d3d9c1593dffce64ab4","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-14 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11273768","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12465486","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12465486","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12465486/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01067-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01067-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01067-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1224945033","display_name":null,"funder_award_id":"FEDER","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G1650125035","display_name":null,"funder_award_id":"B-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G1891403524","display_name":null,"funder_award_id":"PRTR-C17.I1","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G2166634996","display_name":null,"funder_award_id":"PRTR-C17.I1","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2262748287","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G2660406951","display_name":null,"funder_award_id":"/ AEI/10","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G2708301916","display_name":null,"funder_award_id":"2023 FI-100278","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G2988934680","display_name":null,"funder_award_id":"PRTR-C17.I1","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G3005324705","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320321505","funder_display_name":"Generalitat de Catalunya"},{"id":"https://openalex.org/G3025668325","display_name":null,"funder_award_id":"RB-I00","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3429648993","display_name":null,"funder_award_id":"PID202","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3480869486","display_name":null,"funder_award_id":"13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3681454997","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4042783231","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4126322094","display_name":null,"funder_award_id":"01100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G4344171801","display_name":null,"funder_award_id":"PDC2021-121544-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G4816244515","display_name":null,"funder_award_id":"FEDER","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G495392292","display_name":null,"funder_award_id":"FEDER","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G531036588","display_name":null,"funder_award_id":"C17.I1","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5421974903","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G5499608741","display_name":null,"funder_award_id":"MCIN/AEI","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G5550858994","display_name":null,"funder_award_id":"AEI/10","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G5805502524","display_name":null,"funder_award_id":"PID2020","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G6532473816","display_name":null,"funder_award_id":"PRTR-C17.I1","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G6589649124","display_name":null,"funder_award_id":"PID2020-","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G661330594","display_name":null,"funder_award_id":"00110","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G663690589","display_name":null,"funder_award_id":"PID2023-152706OB-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G6685425346","display_name":null,"funder_award_id":"0011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G686748096","display_name":null,"funder_award_id":"PRTR-C17","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7084143925","display_name":null,"funder_award_id":"AEI/10","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7121884764","display_name":null,"funder_award_id":"PID2020-114627RB-I00","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G7266728691","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7553411298","display_name":null,"funder_award_id":"PRTR-C17.I","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7637499251","display_name":null,"funder_award_id":"RTR-C17.I1","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8055432103","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G8260616629","display_name":null,"funder_award_id":"011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G8546142835","display_name":null,"funder_award_id":"PRTR-C17","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321505","display_name":"Generalitat de Catalunya","ror":"https://ror.org/01bg62x04"},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414511184.pdf","grobid_xml":"https://content.openalex.org/works/W4414511184.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1985588649","https://openalex.org/W1998848097","https://openalex.org/W2002063031","https://openalex.org/W2046986600","https://openalex.org/W2056169996","https://openalex.org/W2079953901","https://openalex.org/W2134967712","https://openalex.org/W2161151688","https://openalex.org/W2329592726","https://openalex.org/W2508425869","https://openalex.org/W2536259549","https://openalex.org/W2578175893","https://openalex.org/W2625021681","https://openalex.org/W2800892557","https://openalex.org/W2887981960","https://openalex.org/W2900090807","https://openalex.org/W2920817727","https://openalex.org/W3013426051","https://openalex.org/W3047084383","https://openalex.org/W3107141572","https://openalex.org/W3168430821","https://openalex.org/W3177828909","https://openalex.org/W3202105508","https://openalex.org/W4206509885","https://openalex.org/W4206924409","https://openalex.org/W4221147818","https://openalex.org/W4280541024","https://openalex.org/W4294719209","https://openalex.org/W4297977867","https://openalex.org/W4302307901","https://openalex.org/W4308463927","https://openalex.org/W4310954903","https://openalex.org/W4313260078","https://openalex.org/W4313367649","https://openalex.org/W4315629206","https://openalex.org/W4323652503","https://openalex.org/W4323807713","https://openalex.org/W4383216409","https://openalex.org/W4390113417","https://openalex.org/W4390193806","https://openalex.org/W4390909534","https://openalex.org/W4391673325","https://openalex.org/W4396721167","https://openalex.org/W4404755712"],"related_works":[],"abstract_inverted_index":{"Advances":[0],"in":[1,37,118,129,160,211,233],"docking":[2,38,54,65,100,117,133,148,161,183,209,219],"protocols":[3,39,162,184],"have":[4],"significantly":[5],"enhanced":[6],"the":[7,28,75,79,143,155,167,255],"field":[8],"of":[9,30,45,157,182],"protein-protein":[10],"interaction":[11],"(PPI)":[12],"modulation,":[13],"with":[14,48,70],"AlphaFold2":[15,195,226],"(AF2)":[16],"and":[17,61,72,85,96,132,165,194,201,253],"molecular":[18,198],"dynamics":[19,199],"(MD)":[20],"refinements":[21],"playing":[22],"pivotal":[23],"roles.":[24],"This":[25,176],"study":[26,177],"evaluates":[27],"performance":[29,58,122],"AF2":[31,62,97],"models":[32,227],"against":[33],"experimentally":[34,191],"solved":[35,192],"structures":[36,159,193,232],"targeting":[40,163],"PPIs.":[41],"Using":[42],"a":[43,150,179,246],"dataset":[44],"16":[46],"interactions":[47],"validated":[49],"modulators,":[50],"we":[51,204],"benchmarked":[52],"eight":[53],"protocols,":[55],"revealing":[56],"similar":[57],"between":[59],"native":[60,95,231],"models.":[63,196],"Local":[64],"strategies":[66],"outperformed":[67],"blind":[68],"docking,":[69,235],"TankBind_local":[71],"Glide":[73],"providing":[74],"best":[76],"results":[77,109,244],"across":[78,106],"structural":[80,113,206,267],"types":[81],"tested.":[82],"MD":[83],"simulations":[84],"other":[86],"ensemble":[87],"generation":[88],"algorithms":[89],"such":[90],"as":[91],"AlphaFlow,":[92],"refined":[93],"both":[94,190],"models,":[98],"improving":[99],"outcomes":[101,210],"but":[102,214],"showing":[103],"significant":[104],"variability":[105],"conformations.":[107],"These":[108,152,243],"suggest":[110],"that,":[111],"while":[112],"refinement":[114,207],"can":[115,138],"enhance":[116],"some":[119],"cases,":[120,213],"overall":[121],"appears":[123],"to":[124,169,186,230,263],"be":[125],"constrained":[126,217],"by":[127,218],"limitations":[128],"scoring":[130,172,220,259],"functions":[131],"methodologies.":[134,173],"Although":[135],"protein":[136],"ensembles":[137,200],"improve":[139,170],"virtual":[140,251],"screening,":[141],"predicting":[142],"most":[144],"effective":[145],"conformations":[146],"for":[147,257],"remains":[149,216],"challenge.":[151],"findings":[153],"support":[154],"use":[156],"AF2-generated":[158],"PPIs":[164],"highlight":[166],"need":[168,256],"current":[171],"SCIENTIFIC":[174],"CONTRIBUTION:":[175],"provides":[178],"systematic":[180],"benchmark":[181],"applied":[185],"protein-proteininteractions":[187],"(PPIs)":[188],"using":[189],"Byintegrating":[197],"AlphaFlow-generated":[202],"conformations,":[203],"showthat":[205],"improves":[208],"selected":[212],"overallperformance":[215],"function":[221],"limitations.":[222],"Our":[223],"analysis":[224],"showsthat":[225],"perform":[228],"comparably":[229],"PPI":[234],"validating":[236],"theiruse":[237],"when":[238],"experimental":[239],"data":[240],"are":[241],"unavailable.":[242],"establish":[245],"reference":[247],"framework":[248],"forfuture":[249],"PPI-focused":[250],"screening":[252],"underscore":[254],"improved":[258],"functionsand":[260],"ensemble-based":[261],"approaches":[262],"better":[264],"exploit":[265],"emerging":[266],"prediction":[268],"tools.":[269]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
