{"id":"https://openalex.org/W2968939782","doi":"https://doi.org/10.1093/bioinformatics/btz623","title":"Integrating <i>ab initio</i> and template-based algorithms for protein\u2013protein complex structure prediction","display_name":"Integrating <i>ab initio</i> and template-based algorithms for protein\u2013protein complex structure prediction","publication_year":2019,"publication_date":"2019-08-07","ids":{"openalex":"https://openalex.org/W2968939782","doi":"https://doi.org/10.1093/bioinformatics/btz623","mag":"2968939782","pmid":"https://pubmed.ncbi.nlm.nih.gov/31393558"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz623","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz623","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084924117","display_name":"Sweta Vangaveti","orcid":"https://orcid.org/0000-0002-2274-9544"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sweta Vangaveti","raw_affiliation_strings":["Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester , MA 01605, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester , MA 01605, USA","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065844672","display_name":"Thom Vreven","orcid":"https://orcid.org/0000-0003-3413-806X"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thom Vreven","raw_affiliation_strings":["Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester , MA 01605, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester , MA 01605, USA","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100354659","display_name":"Yang Zhang","orcid":"https://orcid.org/0000-0002-2739-1916"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Zhang","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics , University of Michigan, Ann Arbor, MI 48109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics , University of Michigan, Ann Arbor, MI 48109, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084369008","display_name":"Zhiping Weng","orcid":"https://orcid.org/0000-0002-3032-7966"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhiping Weng","raw_affiliation_strings":["Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester , MA 01605, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester , MA 01605, USA","institution_ids":["https://openalex.org/I166722992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5084369008"],"corresponding_institution_ids":["https://openalex.org/I166722992"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0771,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.76892168,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"36","issue":"3","first_page":"751","last_page":"757"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9679999947547913,"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":0.9679999947547913,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.010200000368058681,"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":0.004699999932199717,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.801593542098999},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7441431879997253},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5207754969596863},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.45210593938827515},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44513049721717834},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.37529343366622925},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34673571586608887},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3321671485900879},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07554134726524353}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.801593542098999},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7441431879997253},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5207754969596863},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.45210593938827515},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44513049721717834},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.37529343366622925},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34673571586608887},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3321671485900879},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07554134726524353},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz623","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz623","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31393558","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31393558","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.umassmed.edu:bioinformatics_pubs-1163","is_oa":false,"landing_page_url":"https://escholarship.umassmed.edu/bioinformatics_pubs/153","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Program in Bioinformatics and Integrative Biology Publications","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G155194203","display_name":null,"funder_award_id":"R01 GM116960","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G758395984","display_name":null,"funder_award_id":"R35 GM136422","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8247244255","display_name":null,"funder_award_id":"R01 GM116960","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1030883578","https://openalex.org/W1538162617","https://openalex.org/W1611787727","https://openalex.org/W1965150339","https://openalex.org/W1968202297","https://openalex.org/W1969327849","https://openalex.org/W1974156712","https://openalex.org/W1976690731","https://openalex.org/W1996183880","https://openalex.org/W2002249897","https://openalex.org/W2010859992","https://openalex.org/W2015059765","https://openalex.org/W2017295384","https://openalex.org/W2019691413","https://openalex.org/W2024103356","https://openalex.org/W2053738633","https://openalex.org/W2055905702","https://openalex.org/W2058813547","https://openalex.org/W2076710572","https://openalex.org/W2085277871","https://openalex.org/W2091710329","https://openalex.org/W2109300715","https://openalex.org/W2110585060","https://openalex.org/W2118514515","https://openalex.org/W2119333768","https://openalex.org/W2128276810","https://openalex.org/W2130754579","https://openalex.org/W2133712572","https://openalex.org/W2139373949","https://openalex.org/W2142895465","https://openalex.org/W2145268834","https://openalex.org/W2153983456","https://openalex.org/W2155005819","https://openalex.org/W2157991822","https://openalex.org/W2160223331","https://openalex.org/W2163614321","https://openalex.org/W2312030690","https://openalex.org/W2554109484","https://openalex.org/W2754890002","https://openalex.org/W2767509030","https://openalex.org/W6679471226","https://openalex.org/W6744701433"],"related_works":["https://openalex.org/W2946599741","https://openalex.org/W2593264178","https://openalex.org/W3171039768","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2058542300","https://openalex.org/W2043066834","https://openalex.org/W1564749278","https://openalex.org/W2294851134","https://openalex.org/W3215498386"],"abstract_inverted_index":{"MOTIVATION:":[0],"Template-based":[1,17],"and":[2,68,101,108,128,133],"template-free":[3,28,79,134],"methods":[4,29,52,135],"have":[5,40],"both":[6],"been":[7,42],"widely":[8],"used":[9],"in":[10],"predicting":[11,33],"the":[12,34,50,84,112],"structures":[13],"of":[14,72,97,106],"protein-protein":[15,56,85],"complexes.":[16],"modeling":[18],"is":[19,25,47,136,147],"effective":[20],"when":[21,111],"a":[22,64,73,78,94,123,152],"reliable":[23],"template":[24],"available,":[26],"while":[27],"are":[30,160],"required":[31],"for":[32,149],"binding":[35],"modes":[36],"or":[37],"interfaces":[38],"that":[39,126],"not":[41],"previously":[43],"observed.":[44],"Our":[45],"goal":[46],"to":[48,53,66],"combine":[49,69],"two":[51],"improve":[54],"computational":[55],"complex":[57],"structure":[58],"prediction.":[59],"RESULTS:":[60],"Here,":[61],"we":[62],"present":[63],"method":[65,75,80,91,125,141],"identify":[67],"high-confidence":[70],"predictions":[71,115,130],"template-based":[74,132],"(SPRING)":[76],"with":[77,103],"(ZDOCK).":[81],"Cross-validated":[82],"using":[83],"docking":[86],"benchmark":[87],"version":[88],"5.0,":[89],"our":[90],"(ZING)":[92],"achieved":[93],"success":[95,104],"rate":[96],"68.2%,":[98],"outperforming":[99],"SPRING":[100],"ZDOCK,":[102],"rates":[105],"52.1%":[107],"35.9%":[109],"respectively,":[110],"top":[113],"10":[114],"were":[116],"considered":[117],"per":[118],"test":[119],"case.":[120],"In":[121],"conclusion,":[122],"statistics-based":[124],"evaluates":[127],"integrates":[129],"from":[131],"more":[137],"successful":[138],"than":[139],"either":[140],"independently.":[142],"AVAILABILITY":[143],"AND":[144],"IMPLEMENTATION:":[145],"ZING":[146],"available":[148,161],"download":[150],"as":[151],"Github":[153],"repository":[154],"(https://github.com/weng-lab/ZING.git).":[155],"SUPPLEMENTARY":[156],"INFORMATION:":[157],"Supplementary":[158],"data":[159],"at":[162],"Bioinformatics":[163],"online.":[164]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2019-08-22T00:00:00"}