{"id":"https://openalex.org/W2060387125","doi":"https://doi.org/10.1145/2147805.2147866","title":"Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces","display_name":"Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces","publication_year":2011,"publication_date":"2011-08-01","ids":{"openalex":"https://openalex.org/W2060387125","doi":"https://doi.org/10.1145/2147805.2147866","mag":"2060387125","pmid":"https://pubmed.ncbi.nlm.nih.gov/25905110"},"language":"en","primary_location":{"id":"doi:10.1145/2147805.2147866","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147866","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4403796","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086880868","display_name":"Li C. Xue","orcid":"https://orcid.org/0000-0002-2613-538X"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li C. Xue","raw_affiliation_strings":["Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028462636","display_name":"Rafael A. Jordan","orcid":null},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]},{"id":"https://openalex.org/I233745408","display_name":"Pontificia Universidad Javeriana","ror":"https://ror.org/03etyjw28","country_code":"CO","type":"education","lineage":["https://openalex.org/I233745408"]}],"countries":["CO","US"],"is_corresponding":false,"raw_author_name":"Rafael A. Jordan","raw_affiliation_strings":["Iowa State University, Ames, IA, and Pontificia Universidad Javeriana, Cali, Colombia","Iowa State University, Ames, IA, and Pontificia Universidad Javeriana, Cali, Colombia#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA, and Pontificia Universidad Javeriana, Cali, Colombia","institution_ids":["https://openalex.org/I233745408"]},{"raw_affiliation_string":"Iowa State University, Ames, IA, and Pontificia Universidad Javeriana, Cali, Colombia#TAB#","institution_ids":["https://openalex.org/I233745408","https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079233454","display_name":"Yasser EL\u2010Manzalawy","orcid":"https://orcid.org/0000-0002-4681-7994"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]},{"id":"https://openalex.org/I184834183","display_name":"Al-Azhar University","ror":"https://ror.org/05fnp1145","country_code":"EG","type":"education","lineage":["https://openalex.org/I184834183"]}],"countries":["EG","US"],"is_corresponding":false,"raw_author_name":"Yasser El-Manzalawy","raw_affiliation_strings":["Iowa State University, Ames, IA, and AI-Azhar University, Cairo, Egypt","Iowa State University, Ames, IA, and AI-Azhar University, Cairo, Egypt#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA, and AI-Azhar University, Cairo, Egypt","institution_ids":["https://openalex.org/I184834183","https://openalex.org/I173911158"]},{"raw_affiliation_string":"Iowa State University, Ames, IA, and AI-Azhar University, Cairo, Egypt#TAB#","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074103258","display_name":"Drena Dobbs","orcid":"https://orcid.org/0000-0003-4404-9554"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Drena Dobbs","raw_affiliation_strings":["Iowa State University, Ames, IA, and Iowa State University, Ames"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA, and Iowa State University, Ames","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004737962","display_name":"Vasant Honavar","orcid":"https://orcid.org/0000-0001-5399-3489"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vasant Honavar","raw_affiliation_strings":["Iowa State University, Ames, IA, and Iowa State University, Ames, IA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Iowa State University, Ames, IA, and Iowa State University, Ames, IA","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6653,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.68719206,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"2011","issue":null,"first_page":"441","last_page":"445"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980999827384949,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980999827384949,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9943000078201294,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9804999828338623,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.8251758813858032},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5188978314399719},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5188176035881042},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.5142814517021179},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.5052905678749084},{"id":"https://openalex.org/keywords/macromolecular-docking","display_name":"Macromolecular docking","score":0.5022432804107666},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4809695780277252},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.43496400117874146},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4349145293235779},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.43328607082366943},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3340936303138733},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2679018974304199},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.2605757713317871},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.20739305019378662},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.19973021745681763},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.190135657787323},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.16941606998443604}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8251758813858032},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5188978314399719},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5188176035881042},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.5142814517021179},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.5052905678749084},{"id":"https://openalex.org/C116887118","wikidata":"https://www.wikidata.org/wiki/Q836685","display_name":"Macromolecular docking","level":3,"score":0.5022432804107666},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4809695780277252},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.43496400117874146},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4349145293235779},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.43328607082366943},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3340936303138733},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2679018974304199},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.2605757713317871},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.20739305019378662},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.19973021745681763},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.190135657787323},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.16941606998443604},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1145/2147805.2147866","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2147805.2147866","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":"proceedings-article"},{"id":"pmid:25905110","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25905110","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":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4403796","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4403796","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM BCB","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4403796","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4403796","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ACM BCB","raw_type":"Text"},"sustainable_development_goals":[{"score":0.47999998927116394,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G2844798518","display_name":null,"funder_award_id":"GM066387","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1565746575","https://openalex.org/W2014890100","https://openalex.org/W2018347124","https://openalex.org/W2038542598","https://openalex.org/W2102312699","https://openalex.org/W2103729016","https://openalex.org/W2109300715","https://openalex.org/W2112743424","https://openalex.org/W2123375001","https://openalex.org/W2141627824","https://openalex.org/W2150399099","https://openalex.org/W2151096117","https://openalex.org/W2152521138","https://openalex.org/W2162682281","https://openalex.org/W2170421654","https://openalex.org/W2171249995","https://openalex.org/W2915344963","https://openalex.org/W2997546679"],"related_works":["https://openalex.org/W1489925612","https://openalex.org/W4400485740","https://openalex.org/W2533022751","https://openalex.org/W3011103292","https://openalex.org/W3187431608","https://openalex.org/W1974422922","https://openalex.org/W2078688023","https://openalex.org/W2163614321","https://openalex.org/W4309353019","https://openalex.org/W4247206618"],"abstract_inverted_index":{"Computational":[0],"protein-protein":[1,86],"docking":[2,29,181],"is":[3,163,198],"a":[4,32,39,57,62,79,104,113],"valuable":[5],"tool":[6],"for":[7,42,83,175,183,194],"determining":[8],"the":[9,21,48,53,67,101,122,125,138,152,155,179],"conformation":[10,59],"of":[11,24,50,56,64,69,103,121,124,131,154,157,178,191],"complexes":[12,182],"formed":[13,60],"by":[14,28,61,89],"interacting":[15,97,132],"proteins.":[16,98],"Selecting":[17],"near-native":[18],"conformations":[19,45,159],"from":[20,95],"large":[22],"number":[23],"possible":[25],"models":[26,197],"generated":[27],"software":[30],"presents":[31],"significant":[33],"challenge":[34],"in":[35],"practice.":[36],"We":[37],"introduce":[38],"novel":[40],"method":[41,162,193],"ranking":[43,156,195],"docked":[44,58,158,196],"based":[46,116],"on":[47,78,117,146],"degree":[49],"overlap":[51],"between":[52,73],"interface":[54,71,87,119,187],"residues":[55,72,88,102,120],"pair":[63],"proteins":[65,133],"with":[66,112],"set":[68],"predicted":[70],"them.":[74],"Our":[75,144],"approach":[76],"relies":[77],"method,":[80],"called":[81],"PS-HomPPI,":[82],"reliably":[84],"predicting":[85],"taking":[90],"into":[91],"account":[92],"information":[93],"derived":[94],"both":[96],"PS-HomPPI":[99,185],"infers":[100],"query":[105,139],"protein":[106,115,127,140],"that":[107,134,151,167],"are":[108,135],"likely":[109],"to":[110,137,166],"interact":[111],"partner":[114,142],"known":[118],"homo-interologs":[123],"query-partner":[126],"pair,":[128],"i.e.,":[129],"pairs":[130],"homologous":[136],"and":[141,172],"protein.":[143],"results":[145],"Docking":[147],"Benchmark":[148],"3.0":[149],"show":[150],"quality":[153],"using":[160,169],"our":[161,192],"consistently":[164],"superior":[165],"produced":[168],"ClusPro":[170],"cluster-size-based":[171],"energy-based":[173],"criteria":[174],"61":[176],"out":[177],"64":[180],"which":[184],"produces":[186],"predictions.":[188],"An":[189],"implementation":[190],"freely":[199],"available":[200],"at:":[201],"http://einstein.cs.iastate.edu/DockRank/.":[202]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2016-06-24T00:00:00"}