{"id":"https://openalex.org/W3165201217","doi":"https://doi.org/10.1093/bioinformatics/btab425","title":"Structural discrimination analysis for constraint selection in protein modeling","display_name":"Structural discrimination analysis for constraint selection in protein modeling","publication_year":2021,"publication_date":"2021-06-03","ids":{"openalex":"https://openalex.org/W3165201217","doi":"https://doi.org/10.1093/bioinformatics/btab425","mag":"3165201217"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab425","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab425","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"],"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/A5093558880","display_name":"Guilherme Fahur Bottino","orcid":"https://orcid.org/0000-0003-1953-1576"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Guilherme F Bottino","raw_affiliation_strings":["Center for Computational Engineering & Science, University of Campinas , Campinas, SP,","Institute of Chemistry, University of Campinas , Campinas, SP,","Center for Computational Engineering & Science, University of Campinas , Campinas, SP, Brazil","Institute of Chemistry, University of Campinas , Campinas, SP, Brazil"],"affiliations":[{"raw_affiliation_string":"Center for Computational Engineering & Science, University of Campinas , Campinas, SP,","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Institute of Chemistry, University of Campinas , Campinas, SP,","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Center for Computational Engineering & Science, University of Campinas , Campinas, SP, Brazil","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Institute of Chemistry, University of Campinas , Campinas, SP, Brazil","institution_ids":["https://openalex.org/I181391015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074602740","display_name":"A. Ferrari","orcid":"https://orcid.org/0000-0002-9199-2257"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Allan J R Ferrari","raw_affiliation_strings":["Center for Computational Engineering & Science, University of Campinas , Campinas, SP,","Institute of Chemistry, University of Campinas , Campinas, SP,","Institute of Chemistry, University of Campinas , Campinas, SP, Brazil","Center for Computational Engineering & Science, University of Campinas , Campinas, SP, Brazil"],"affiliations":[{"raw_affiliation_string":"Center for Computational Engineering & Science, University of Campinas , Campinas, SP,","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Institute of Chemistry, University of Campinas , Campinas, SP,","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Institute of Chemistry, University of Campinas , Campinas, SP, Brazil","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Center for Computational Engineering & Science, University of Campinas , Campinas, SP, Brazil","institution_ids":["https://openalex.org/I181391015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038331268","display_name":"F\u00e1bio C. Gozzo","orcid":"https://orcid.org/0000-0002-5270-4427"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Fabio C Gozzo","raw_affiliation_strings":["Institute of Chemistry, University of Campinas , Campinas, SP,","Institute of Chemistry, University of Campinas , Campinas, SP, Brazil"],"affiliations":[{"raw_affiliation_string":"Institute of Chemistry, University of Campinas , Campinas, SP,","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Institute of Chemistry, University of Campinas , Campinas, SP, Brazil","institution_ids":["https://openalex.org/I181391015"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019517261","display_name":"Leandro Mart\u0131\u0301nez","orcid":"https://orcid.org/0000-0002-6857-1884"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Leandro Mart\u00ednez","raw_affiliation_strings":["Center for Computational Engineering & Science, University of Campinas , Campinas, SP,","Institute of Chemistry, University of Campinas , Campinas, SP,","Institute of Chemistry, University of Campinas , Campinas, SP, Brazil","Center for Computational Engineering & Science, University of Campinas , Campinas, SP, Brazil"],"affiliations":[{"raw_affiliation_string":"Center for Computational Engineering & Science, University of Campinas , Campinas, SP,","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Institute of Chemistry, University of Campinas , Campinas, SP,","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Institute of Chemistry, University of Campinas , Campinas, SP, Brazil","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Center for Computational Engineering & Science, University of Campinas , Campinas, SP, Brazil","institution_ids":["https://openalex.org/I181391015"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5019517261"],"corresponding_institution_ids":["https://openalex.org/I181391015"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0813,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.43097837,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"37","issue":"21","first_page":"3766","last_page":"3773"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9988999962806702,"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":0.9988999962806702,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9988999962806702,"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":0.9968000054359436,"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/constraint","display_name":"Constraint (computer-aided design)","score":0.7534838318824768},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.689527153968811},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5455498099327087},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.46264684200286865},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.43000710010528564},{"id":"https://openalex.org/keywords/redundancy","display_name":"Redundancy (engineering)","score":0.42888593673706055},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4270763099193573},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34422963857650757},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32605788111686707},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17676177620887756}],"concepts":[{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.7534838318824768},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.689527153968811},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5455498099327087},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.46264684200286865},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.43000710010528564},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.42888593673706055},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4270763099193573},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34422963857650757},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32605788111686707},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17676177620887756},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btab425","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab425","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"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.6600000262260437}],"awards":[{"id":"https://openalex.org/G3717411714","display_name":null,"funder_award_id":"2010/16947-9","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G4030283353","display_name":null,"funder_award_id":"2018/14274-9","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G4208676761","display_name":null,"funder_award_id":"2018/24293-0","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G4253322330","display_name":null,"funder_award_id":"2016/13195-2","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G5223555579","display_name":null,"funder_award_id":"2019/17007-4","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"},{"id":"https://openalex.org/G7979888459","display_name":null,"funder_award_id":"140317/2019-8","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G8974603849","display_name":null,"funder_award_id":"2013/08293-7","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"}],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W1493324970","https://openalex.org/W1895528264","https://openalex.org/W1946569870","https://openalex.org/W1987158549","https://openalex.org/W1995017064","https://openalex.org/W2008545402","https://openalex.org/W2021876859","https://openalex.org/W2044357547","https://openalex.org/W2045288235","https://openalex.org/W2051091550","https://openalex.org/W2056668858","https://openalex.org/W2061042699","https://openalex.org/W2065921821","https://openalex.org/W2079327388","https://openalex.org/W2085658801","https://openalex.org/W2093769098","https://openalex.org/W2101291993","https://openalex.org/W2107867854","https://openalex.org/W2114340287","https://openalex.org/W2115167726","https://openalex.org/W2115540209","https://openalex.org/W2117020466","https://openalex.org/W2119843684","https://openalex.org/W2120162409","https://openalex.org/W2121444044","https://openalex.org/W2125725340","https://openalex.org/W2126711803","https://openalex.org/W2127322768","https://openalex.org/W2135338948","https://openalex.org/W2152561142","https://openalex.org/W2154389376","https://openalex.org/W2161151688","https://openalex.org/W2163000619","https://openalex.org/W2166701319","https://openalex.org/W2171641243","https://openalex.org/W2275780625","https://openalex.org/W2327188017","https://openalex.org/W2519539312","https://openalex.org/W2573143651","https://openalex.org/W2574496196","https://openalex.org/W2750791471","https://openalex.org/W2765742208","https://openalex.org/W2772277708","https://openalex.org/W2791711082","https://openalex.org/W2804523481","https://openalex.org/W2809682566","https://openalex.org/W2897174070","https://openalex.org/W2898402099","https://openalex.org/W2949867299","https://openalex.org/W2951621517","https://openalex.org/W2960589734","https://openalex.org/W2962831078","https://openalex.org/W2965351431","https://openalex.org/W2977360892","https://openalex.org/W2979866130","https://openalex.org/W2985961606","https://openalex.org/W2997234557","https://openalex.org/W2999044305","https://openalex.org/W3199799076","https://openalex.org/W4249733541","https://openalex.org/W6701507866","https://openalex.org/W6769886907"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W188202134","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W4255934811","https://openalex.org/W2465382974","https://openalex.org/W2010229520"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Protein":[2],"structure":[3,26],"modeling":[4,150,197],"can":[5],"be":[6],"improved":[7,127],"by":[8,121,128],"the":[9,28,38,47,58,63,87,103,110,152,157,160,165,177,180,204,216,224,236],"use":[10,172],"of":[11,27,37,60,72,98,105,130,159,167,173,179,182,218],"distance":[12],"constraints":[13,61],"between":[14],"amino":[15],"acid":[16],"residues,":[17],"provided":[18],"such":[19],"data":[20,214,245],"reflects\u2014at":[21],"least":[22],"partially\u2014the":[23],"native":[24,39],"tertiary":[25],"target":[29],"system.":[30],"In":[31,74],"fact,":[32],"only":[33,140],"a":[34,79,186],"small":[35],"subset":[36],"contact":[40,118],"map":[41],"is":[42,55,185,209,233],"necessary":[43],"to":[44,56,100,192],"successfully":[45],"drive":[46],"model":[48],"conformational":[49,111],"search,":[50],"so":[51],"one":[52],"important":[53],"goal":[54],"obtain":[57],"set":[59,162],"with":[62,147,189],"highest":[64],"true-positive":[65],"rate,":[66],"lowest":[67],"redundancy":[68],"and":[69,82,163,196,200,230,232],"greatest":[70],"amount":[71],"information.":[73],"this":[75,207,219],"work,":[76],"we":[77],"introduce":[78],"constraint":[80,107,154,161,183,194],"evaluation":[81],"selection":[83,158],"method":[84],"based":[85],"on":[86,211,240],"point-biserial":[88],"correlation":[89],"coefficient,":[90],"which":[91],"utilizes":[92],"structural":[93],"information":[94,181,243],"from":[95,235],"an":[96,148],"ensemble":[97],"models":[99],"indirectly":[101],"measure":[102],"power":[104],"each":[106],"in":[108,134,141,206,228],"biasing":[109],"search":[112],"toward":[113],"consensus":[114],"structures.":[115],"Results":[116],"Residue":[117],"maps":[119],"obtained":[120],"direct":[122],"coupling":[123],"analysis":[124,175],"are":[125,246],"systematically":[126],"means":[129],"discriminant":[131,174],"analysis,":[132],"reaching":[133],"some":[135],"cases":[136],"accuracies":[137],"often":[138],"seen":[139],"modern":[142],"deep-learning-based":[143],"approaches.":[144],"When":[145],"combined":[146],"iterative":[149],"workflow,":[151],"proposed":[153],"classification":[155],"optimizes":[156],"maximizes":[164],"probability":[166],"obtaining":[168],"successful":[169],"models.":[170],"The":[171],"for":[176,203,226],"valorization":[178],"datasets":[184],"general":[187],"concept":[188],"possible":[190],"applications":[191],"other":[193],"types":[195],"problems.":[198],"Availability":[199],"implementation":[201],"MSA":[202],"targets":[205],"work":[208],"available":[210,234,247],"https://github.com/m3g/2021_Bottino_Biserial.":[212],"Modeling":[213],"supporting":[215],"findings":[217],"study":[220],"was":[221],"generated":[222],"at":[223,248],"Center":[225],"Computing":[227],"Engineering":[229],"Sciences,":[231],"corresponding":[237],"author":[238],"LM":[239],"request.":[241],"Supplementary":[242,244],"Bioinformatics":[249],"online.":[250]},"counts_by_year":[{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2021-06-07T00:00:00"}
