{"id":"https://openalex.org/W2020575338","doi":"https://doi.org/10.1021/ci100265x","title":"Protein\u2212Protein Binding Site Prediction by Local Structural Alignment","display_name":"Protein\u2212Protein Binding Site Prediction by Local Structural Alignment","publication_year":2010,"publication_date":"2010-10-04","ids":{"openalex":"https://openalex.org/W2020575338","doi":"https://doi.org/10.1021/ci100265x","mag":"2020575338","pmid":"https://pubmed.ncbi.nlm.nih.gov/20919700"},"language":"en","primary_location":{"id":"doi:10.1021/ci100265x","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100265x","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/A5053488630","display_name":"Nejc Carl","orcid":null},"institutions":[{"id":"https://openalex.org/I118905719","display_name":"University of Primorska","ror":"https://ror.org/05xefg082","country_code":"SI","type":"education","lineage":["https://openalex.org/I118905719"]},{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Nejc Carl","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia","institution_ids":["https://openalex.org/I118905719","https://openalex.org/I4210152560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007997462","display_name":"Janez Konc","orcid":"https://orcid.org/0000-0003-0160-3375"},"institutions":[{"id":"https://openalex.org/I118905719","display_name":"University of Primorska","ror":"https://ror.org/05xefg082","country_code":"SI","type":"education","lineage":["https://openalex.org/I118905719"]},{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Janez Konc","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia","institution_ids":["https://openalex.org/I118905719","https://openalex.org/I4210152560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065054584","display_name":"Bla\u017e Vehar","orcid":null},"institutions":[{"id":"https://openalex.org/I118905719","display_name":"University of Primorska","ror":"https://ror.org/05xefg082","country_code":"SI","type":"education","lineage":["https://openalex.org/I118905719"]},{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":false,"raw_author_name":"Bla\u017e Vehar","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia","institution_ids":["https://openalex.org/I118905719","https://openalex.org/I4210152560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074495088","display_name":"Du\u0161anka Jane\u017ei\u010d","orcid":"https://orcid.org/0000-0003-4067-0116"},"institutions":[{"id":"https://openalex.org/I118905719","display_name":"University of Primorska","ror":"https://ror.org/05xefg082","country_code":"SI","type":"education","lineage":["https://openalex.org/I118905719"]},{"id":"https://openalex.org/I4210152560","display_name":"National Institute of Chemistry","ror":"https://ror.org/050mac570","country_code":"SI","type":"facility","lineage":["https://openalex.org/I4210152560"]}],"countries":["SI"],"is_corresponding":true,"raw_author_name":"Du\u0161anka Jane\u017ei\u010d","raw_affiliation_strings":["National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia, and Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagolja\u0161ka 8, SI-6000 Koper, Slovenia","institution_ids":["https://openalex.org/I118905719","https://openalex.org/I4210152560"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074495088"],"corresponding_institution_ids":["https://openalex.org/I118905719","https://openalex.org/I4210152560"],"apc_list":null,"apc_paid":null,"fwci":0.8055,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.70953195,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"50","issue":"10","first_page":"1906","last_page":"1913"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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":0.9990000128746033,"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":0.9984999895095825,"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":0.9940999746322632,"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/protein-structure","display_name":"Protein structure","score":0.4763919711112976},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42297613620758057},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4187600612640381},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3282477855682373},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.29515790939331055},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21085035800933838},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15517818927764893}],"concepts":[{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4763919711112976},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42297613620758057},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4187600612640381},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3282477855682373},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.29515790939331055},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21085035800933838},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15517818927764893}],"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci100265x","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100265x","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:20919700","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20919700","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322554","display_name":"Javna Agencija za Raziskovalno Dejavnost RS","ror":"https://ror.org/059bp8k51"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1965910641","https://openalex.org/W1971618381","https://openalex.org/W1980209352","https://openalex.org/W1999758645","https://openalex.org/W2006421122","https://openalex.org/W2021954541","https://openalex.org/W2029101636","https://openalex.org/W2033855745","https://openalex.org/W2040495488","https://openalex.org/W2043699100","https://openalex.org/W2044359120","https://openalex.org/W2056756773","https://openalex.org/W2057813163","https://openalex.org/W2057849368","https://openalex.org/W2080249432","https://openalex.org/W2098869926","https://openalex.org/W2099013368","https://openalex.org/W2104760790","https://openalex.org/W2106449850","https://openalex.org/W2108067237","https://openalex.org/W2124904677","https://openalex.org/W2130479394","https://openalex.org/W2136525667","https://openalex.org/W2136832587","https://openalex.org/W2138770756","https://openalex.org/W2141627824","https://openalex.org/W2146940292","https://openalex.org/W2148219066","https://openalex.org/W2157892451","https://openalex.org/W2167315103","https://openalex.org/W2195959843"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"Generalization":[0],"of":[1,10,18,91,105],"an":[2],"earlier":[3],"algorithm":[4],"has":[5,45],"led":[6],"to":[7,30,48,61,79],"the":[8,42,50,53,56,81,89],"development":[9],"new":[11,43],"local":[12,101],"structural":[13,39,73,102],"alignment":[14],"algorithms":[15,23,44],"for":[16,38],"prediction":[17],"protein-protein":[19],"binding":[20,83,93],"sites.":[21,84],"The":[22,36,71],"use":[24],"maximum":[25],"cliques":[26],"on":[27],"protein":[28,34,58,82,92,107],"graphs":[29],"define":[31],"structurally":[32],"similar":[33],"regions.":[35],"search":[37],"neighbors":[40],"in":[41,52],"been":[46],"extended":[47],"all":[49],"proteins":[51,65],"PDB":[54],"and":[55,77],"query":[57],"is":[59],"compared":[60],"more":[62],"than":[63],"60,000":[64],"or":[66],"over":[67],"300,000":[68],"single-chain":[69],"structures.":[70],"resulting":[72],"similarities":[74,103],"are":[75],"combined":[76],"used":[78],"predict":[80],"This":[85],"study":[86],"shows":[87],"that":[88],"location":[90],"sites":[94],"can":[95],"be":[96],"predicted":[97],"by":[98],"comparing":[99],"only":[100],"irrespective":[104],"general":[106],"folds.":[108]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2012,"cited_by_count":4}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
