{"id":"https://openalex.org/W2396235019","doi":"https://doi.org/10.1021/acs.jcim.5b00190","title":"IChemPIC: A Random Forest Classifier of Biological and Crystallographic Protein\u2013Protein Interfaces","display_name":"IChemPIC: A Random Forest Classifier of Biological and Crystallographic Protein\u2013Protein Interfaces","publication_year":2015,"publication_date":"2015-09-07","ids":{"openalex":"https://openalex.org/W2396235019","doi":"https://doi.org/10.1021/acs.jcim.5b00190","mag":"2396235019","pmid":"https://pubmed.ncbi.nlm.nih.gov/26344157"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5b00190","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00190","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5113878118","display_name":"Franck Da Silva","orcid":null},"institutions":[{"id":"https://openalex.org/I4210116974","display_name":"Laboratoire d'Innovation Th\u00e9rapeutique","ror":"https://ror.org/02g4mxc89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210116974","https://openalex.org/I4210128300","https://openalex.org/I68947357"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I68947357","display_name":"Universit\u00e9 de Strasbourg","ror":"https://ror.org/00pg6eq24","country_code":"FR","type":"education","lineage":["https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Franck Da Silva","raw_affiliation_strings":["Laboratoire d\u2019Innovation\rTh\u00e9rapeutique, UMR 7200 CNRS\u2212Universit\u00e9 de Strasbourg, 67400 Illkirch, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire d\u2019Innovation\rTh\u00e9rapeutique, UMR 7200 CNRS\u2212Universit\u00e9 de Strasbourg, 67400 Illkirch, France","institution_ids":["https://openalex.org/I4210116974","https://openalex.org/I68947357","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090712916","display_name":"J\u00e9r\u00e9my Desaphy","orcid":"https://orcid.org/0000-0002-6860-0825"},"institutions":[{"id":"https://openalex.org/I68947357","display_name":"Universit\u00e9 de Strasbourg","ror":"https://ror.org/00pg6eq24","country_code":"FR","type":"education","lineage":["https://openalex.org/I68947357"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210116974","display_name":"Laboratoire d'Innovation Th\u00e9rapeutique","ror":"https://ror.org/02g4mxc89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210116974","https://openalex.org/I4210128300","https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"J\u00e9r\u00e9my Desaphy","raw_affiliation_strings":["Laboratoire d\u2019Innovation\rTh\u00e9rapeutique, UMR 7200 CNRS\u2212Universit\u00e9 de Strasbourg, 67400 Illkirch, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire d\u2019Innovation\rTh\u00e9rapeutique, UMR 7200 CNRS\u2212Universit\u00e9 de Strasbourg, 67400 Illkirch, France","institution_ids":["https://openalex.org/I4210116974","https://openalex.org/I68947357","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077272199","display_name":"Guillaume Bret","orcid":"https://orcid.org/0000-0001-5434-0906"},"institutions":[{"id":"https://openalex.org/I68947357","display_name":"Universit\u00e9 de Strasbourg","ror":"https://ror.org/00pg6eq24","country_code":"FR","type":"education","lineage":["https://openalex.org/I68947357"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210116974","display_name":"Laboratoire d'Innovation Th\u00e9rapeutique","ror":"https://ror.org/02g4mxc89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210116974","https://openalex.org/I4210128300","https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Guillaume Bret","raw_affiliation_strings":["Laboratoire d\u2019Innovation\rTh\u00e9rapeutique, UMR 7200 CNRS\u2212Universit\u00e9 de Strasbourg, 67400 Illkirch, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire d\u2019Innovation\rTh\u00e9rapeutique, UMR 7200 CNRS\u2212Universit\u00e9 de Strasbourg, 67400 Illkirch, France","institution_ids":["https://openalex.org/I4210116974","https://openalex.org/I68947357","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037175705","display_name":"Didier Rognan","orcid":"https://orcid.org/0000-0002-0577-641X"},"institutions":[{"id":"https://openalex.org/I68947357","display_name":"Universit\u00e9 de Strasbourg","ror":"https://ror.org/00pg6eq24","country_code":"FR","type":"education","lineage":["https://openalex.org/I68947357"]},{"id":"https://openalex.org/I4210116974","display_name":"Laboratoire d'Innovation Th\u00e9rapeutique","ror":"https://ror.org/02g4mxc89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210116974","https://openalex.org/I4210128300","https://openalex.org/I68947357"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Didier Rognan","raw_affiliation_strings":["Laboratoire d\u2019Innovation\rTh\u00e9rapeutique, UMR 7200 CNRS\u2212Universit\u00e9 de Strasbourg, 67400 Illkirch, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire d\u2019Innovation\rTh\u00e9rapeutique, UMR 7200 CNRS\u2212Universit\u00e9 de Strasbourg, 67400 Illkirch, France","institution_ids":["https://openalex.org/I4210116974","https://openalex.org/I68947357","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5113878118"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I4210116974","https://openalex.org/I68947357"],"apc_list":null,"apc_paid":null,"fwci":3.8557,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.94095163,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"55","issue":"9","first_page":"2005","last_page":"2014"},"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":0.9979000091552734,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9771999716758728,"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/random-forest","display_name":"Random forest","score":0.7570191621780396},{"id":"https://openalex.org/keywords/prioritization","display_name":"Prioritization","score":0.7122057676315308},{"id":"https://openalex.org/keywords/druggability","display_name":"Druggability","score":0.6412992477416992},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5161717534065247},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5061160922050476},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.46854886412620544},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.455424964427948},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.420958936214447},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3805120885372162},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.32248538732528687},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29013770818710327},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2037971019744873},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12892159819602966},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09201446175575256}],"concepts":[{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.7570191621780396},{"id":"https://openalex.org/C2777615720","wikidata":"https://www.wikidata.org/wiki/Q11888847","display_name":"Prioritization","level":2,"score":0.7122057676315308},{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.6412992477416992},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5161717534065247},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5061160922050476},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.46854886412620544},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.455424964427948},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.420958936214447},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3805120885372162},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.32248538732528687},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29013770818710327},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2037971019744873},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12892159819602966},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09201446175575256},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","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}],"mesh":[{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020395","descriptor_name":"Receptors, Interleukin-7","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020395","descriptor_name":"Receptors, Interleukin-7","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020395","descriptor_name":"Receptors, Interleukin-7","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000295","qualifier_name":"instrumentation","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5b00190","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00190","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:26344157","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26344157","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 chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6899999976158142,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1915490970","https://openalex.org/W1951252517","https://openalex.org/W1977845138","https://openalex.org/W1985153601","https://openalex.org/W1992806534","https://openalex.org/W1997655258","https://openalex.org/W2035503835","https://openalex.org/W2036282817","https://openalex.org/W2041026060","https://openalex.org/W2041877730","https://openalex.org/W2042153350","https://openalex.org/W2045501270","https://openalex.org/W2056169996","https://openalex.org/W2057810258","https://openalex.org/W2058017150","https://openalex.org/W2072435450","https://openalex.org/W2072582089","https://openalex.org/W2081598613","https://openalex.org/W2094018539","https://openalex.org/W2098416804","https://openalex.org/W2098869926","https://openalex.org/W2100543317","https://openalex.org/W2100598991","https://openalex.org/W2102791444","https://openalex.org/W2108715648","https://openalex.org/W2108862316","https://openalex.org/W2112804624","https://openalex.org/W2124036707","https://openalex.org/W2130479394","https://openalex.org/W2135428461","https://openalex.org/W2150577353","https://openalex.org/W2155589321","https://openalex.org/W2158100564","https://openalex.org/W2170048458","https://openalex.org/W2911964244","https://openalex.org/W4235295213","https://openalex.org/W4245193008","https://openalex.org/W4255136093"],"related_works":["https://openalex.org/W2222429409","https://openalex.org/W2735553727","https://openalex.org/W2101288419","https://openalex.org/W2559132852","https://openalex.org/W2208268900","https://openalex.org/W2067712920","https://openalex.org/W2914490533","https://openalex.org/W2021213676","https://openalex.org/W1832993298","https://openalex.org/W1970785155"],"abstract_inverted_index":{"Protein-protein":[0],"interactions":[1],"are":[2],"becoming":[3],"a":[4,39,64,137],"major":[5],"focus":[6],"of":[7,27,30,49,66,84,98,113,140],"academic":[8],"and":[9,46,130],"pharmaceutical":[10],"research":[11],"to":[12,19,41,80,96,136,148],"identify":[13],"low":[14],"molecular":[15,72],"weight":[16],"compounds":[17],"able":[18,79],"modulate":[20],"oligomeric":[21,141],"signaling":[22],"complexes.":[23],"As":[24],"the":[25,82,99,110],"number":[26],"protein":[28],"complexes":[29,142],"known":[31],"three-dimensional":[32],"structure":[33],"is":[34,38,78,120],"constantly":[35],"increasing,":[36],"there":[37],"need":[40],"discard":[42],"biologically":[43],"irrelevant":[44],"interfaces":[45,69,87,147],"prioritize":[47],"those":[48],"high":[50],"value":[51],"for":[52],"potential":[53],"druggability":[54],"assessment.":[55],"A":[56],"Random":[57],"Forest":[58],"model":[59],"has":[60],"been":[61],"trained":[62],"on":[63],"set":[65],"300":[67],"protein-protein":[68,116],"using":[70],"45":[71],"interaction":[73],"descriptors":[74],"as":[75],"input.":[76],"It":[77],"predict":[81],"nature":[83],"external":[85],"test":[86],"(crystallographic":[88],"vs":[89],"biological)":[90],"with":[91],"accuracy":[92],"at":[93],"least":[94],"equal":[95],"that":[97],"best":[100],"state-of-the-art":[101],"methods.":[102],"However,":[103],"our":[104],"method":[105],"presents":[106],"unique":[107],"advantages":[108],"in":[109,123],"early":[111],"prioritization":[112],"potentially":[114],"ligandable":[115],"interfaces:":[117],"(i)":[118],"it":[119,132],"equally":[121],"robust":[122],"predicting":[124],"either":[125],"crystallographic":[126,150],"or":[127],"biological":[128,146],"contacts":[129],"(ii)":[131],"can":[133],"be":[134],"applied":[135],"wide":[138],"array":[139],"ranging":[143],"from":[144],"small-sized":[145],"large":[149],"contacts.":[151]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
