{"id":"https://openalex.org/W2141800650","doi":"https://doi.org/10.1093/nar/gkr1049","title":"ProtChemSI: a network of protein-chemical structural interactions","display_name":"ProtChemSI: a network of protein-chemical structural interactions","publication_year":2011,"publication_date":"2011-11-21","ids":{"openalex":"https://openalex.org/W2141800650","doi":"https://doi.org/10.1093/nar/gkr1049","mag":"2141800650","pmid":"https://pubmed.ncbi.nlm.nih.gov/22110041"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkr1049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr1049","pdf_url":"https://academic.oup.com/nar/article-pdf/40/D1/D549/9476031/gkr1049.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/40/D1/D549/9476031/gkr1049.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101632496","display_name":"Olga V. Kalinina","orcid":"https://orcid.org/0000-0002-9445-477X"},"institutions":[{"id":"https://openalex.org/I4210107660","display_name":"Institute for Information Transmission Problems","ror":"https://ror.org/013w2d378","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210097085","https://openalex.org/I4210107660"]},{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE","RU"],"is_corresponding":false,"raw_author_name":"O. V. Kalinina","raw_affiliation_strings":["Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany","Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, 2Institute for Information Transmission Problems, RAS, Bolshoi Karenty pereulok 19, Moscow, 127994, Russia and 3Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 OWS, UK"],"affiliations":[{"raw_affiliation_string":"Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany","institution_ids":[]},{"raw_affiliation_string":"Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, 2Institute for Information Transmission Problems, RAS, Bolshoi Karenty pereulok 19, Moscow, 127994, Russia and 3Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 OWS, UK","institution_ids":["https://openalex.org/I4210107660","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004501652","display_name":"Ole Wichmann","orcid":"https://orcid.org/0000-0003-2353-7188"},"institutions":[{"id":"https://openalex.org/I4210107660","display_name":"Institute for Information Transmission Problems","ror":"https://ror.org/013w2d378","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210097085","https://openalex.org/I4210107660"]},{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE","RU"],"is_corresponding":false,"raw_author_name":"O. Wichmann","raw_affiliation_strings":["Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, 2Institute for Information Transmission Problems, RAS, Bolshoi Karenty pereulok 19, Moscow, 127994, Russia and 3Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 OWS, UK"],"affiliations":[{"raw_affiliation_string":"Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, 2Institute for Information Transmission Problems, RAS, Bolshoi Karenty pereulok 19, Moscow, 127994, Russia and 3Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 OWS, UK","institution_ids":["https://openalex.org/I4210107660","https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037439081","display_name":"Gordana Apic","orcid":"https://orcid.org/0009-0003-4747-7594"},"institutions":[{"id":"https://openalex.org/I4210107660","display_name":"Institute for Information Transmission Problems","ror":"https://ror.org/013w2d378","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210097085","https://openalex.org/I4210107660"]},{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE","RU"],"is_corresponding":false,"raw_author_name":"G. Apic","raw_affiliation_strings":["Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, 2Institute for Information Transmission Problems, RAS, Bolshoi Karenty pereulok 19, Moscow, 127994, Russia and 3Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 OWS, UK"],"affiliations":[{"raw_affiliation_string":"Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, 2Institute for Information Transmission Problems, RAS, Bolshoi Karenty pereulok 19, Moscow, 127994, Russia and 3Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 OWS, UK","institution_ids":["https://openalex.org/I4210107660","https://openalex.org/I223822909"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108001959","display_name":"Robert B. Russell","orcid":"https://orcid.org/0000-0002-1905-4717"},"institutions":[{"id":"https://openalex.org/I4210107660","display_name":"Institute for Information Transmission Problems","ror":"https://ror.org/013w2d378","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210097085","https://openalex.org/I4210107660"]},{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE","RU"],"is_corresponding":true,"raw_author_name":"R. B. Russell","raw_affiliation_strings":["Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany,","Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, 2Institute for Information Transmission Problems, RAS, Bolshoi Karenty pereulok 19, Moscow, 127994, Russia and 3Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 OWS, UK"],"affiliations":[{"raw_affiliation_string":"Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany,","institution_ids":["https://openalex.org/I223822909"]},{"raw_affiliation_string":"Cell Networks, BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany, 2Institute for Information Transmission Problems, RAS, Bolshoi Karenty pereulok 19, Moscow, 127994, Russia and 3Cambridge Cell Networks Ltd, St John's Innovation Centre, Cowley Road, Cambridge CB4 OWS, UK","institution_ids":["https://openalex.org/I4210107660","https://openalex.org/I223822909"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5108001959"],"corresponding_institution_ids":["https://openalex.org/I223822909","https://openalex.org/I4210107660"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.667,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.69559586,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"40","issue":"D1","first_page":"D549","last_page":"D553"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9984999895095825,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9983999729156494,"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/biology","display_name":"Biology","score":0.9278872013092041},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5260220170021057},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.42017924785614014},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3824054002761841},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3367893099784851},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.23235797882080078}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9278872013092041},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5260220170021057},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.42017924785614014},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3824054002761841},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3367893099784851},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.23235797882080078}],"mesh":[{"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":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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":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":4,"locations":[{"id":"doi:10.1093/nar/gkr1049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr1049","pdf_url":"https://academic.oup.com/nar/article-pdf/40/D1/D549/9476031/gkr1049.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:22110041","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22110041","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:nar:40/D1/D549","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/40/D1/D549","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:3245083","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3245083","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":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkr1049","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr1049","pdf_url":"https://academic.oup.com/nar/article-pdf/40/D1/D549/9476031/gkr1049.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6052429835","display_name":null,"funder_award_id":"(DFG)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2141800650.pdf","grobid_xml":"https://content.openalex.org/works/W2141800650.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W2007287574","https://openalex.org/W2009313526","https://openalex.org/W2024211688","https://openalex.org/W2064154425","https://openalex.org/W2069119991","https://openalex.org/W2092285329","https://openalex.org/W2096864392","https://openalex.org/W2125904022","https://openalex.org/W2127553917","https://openalex.org/W2146465875","https://openalex.org/W2158714788","https://openalex.org/W2166458835"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1971568933","https://openalex.org/W2013243191","https://openalex.org/W2061542922"],"abstract_inverted_index":{"Progress":[0],"in":[1,16],"structure":[2,54],"determination":[3],"methods":[4],"means":[5],"that":[6],"the":[7,38],"set":[8,30],"of":[9,14,31,46],"experimentally":[10],"determined":[11],"3D":[12],"structures":[13,32],"proteins":[15,61],"complex":[17],"with":[18],"small":[19],"molecules":[20],"is":[21,76],"growing":[22],"exponentially.":[23],"ProtChemSI":[24],"exploits":[25],"and":[26,36,68],"extends":[27],"this":[28],"useful":[29],"by":[33,50],"both":[34],"collecting":[35],"annotating":[37],"existing":[39],"data":[40],"as":[41,43],"well":[42],"providing":[44],"models":[45],"potential":[47],"complexes":[48,71],"inferred":[49],"protein":[51],"or":[52],"chemical":[53,66],"similarity.":[55],"The":[56],"database":[57],"currently":[58],"includes":[59],"7704":[60],"from":[62],"1803":[63],"organisms,":[64],"11,324":[65],"compounds":[67],"202,":[69],"289":[70],"including":[72],"178,974":[73],"predicted.":[74],"It":[75],"publicly":[77],"available":[78],"at":[79],"http://pcidb.russelllab.org.":[80]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
