{"id":"https://openalex.org/W2114599399","doi":"https://doi.org/10.1093/bioinformatics/btq504","title":"SimiCon: a web tool for protein\u2013ligand model comparison through calculation of equivalent atomic contacts","display_name":"SimiCon: a web tool for protein\u2013ligand model comparison through calculation of equivalent atomic contacts","publication_year":2010,"publication_date":"2010-09-24","ids":{"openalex":"https://openalex.org/W2114599399","doi":"https://doi.org/10.1093/bioinformatics/btq504","mag":"2114599399","pmid":"https://pubmed.ncbi.nlm.nih.gov/20871105"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq504","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq504","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/21/2784/564496/btq504.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/21/2784/564496/btq504.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023487324","display_name":"Manuel Rueda","orcid":"https://orcid.org/0000-0001-9280-058X"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I40399489","display_name":"Torrey Pines Institute For Molecular Studies","ror":"https://ror.org/01grq2104","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40399489"]},{"id":"https://openalex.org/I4210111989","display_name":"Molsoft (United States)","ror":"https://ror.org/024712k05","country_code":"US","type":"company","lineage":["https://openalex.org/I4210111989"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Manuel Rueda","raw_affiliation_strings":["1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA"],"affiliations":[{"raw_affiliation_string":"1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I40399489","https://openalex.org/I36258959","https://openalex.org/I4210111989"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032022972","display_name":"Vsevolod Katritch","orcid":"https://orcid.org/0000-0003-3883-4505"},"institutions":[{"id":"https://openalex.org/I40399489","display_name":"Torrey Pines Institute For Molecular Studies","ror":"https://ror.org/01grq2104","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40399489"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210111989","display_name":"Molsoft (United States)","ror":"https://ror.org/024712k05","country_code":"US","type":"company","lineage":["https://openalex.org/I4210111989"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vsevolod Katritch","raw_affiliation_strings":["1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA"],"affiliations":[{"raw_affiliation_string":"1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I40399489","https://openalex.org/I36258959","https://openalex.org/I4210111989"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064358366","display_name":"Eugene Raush","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I40399489","display_name":"Torrey Pines Institute For Molecular Studies","ror":"https://ror.org/01grq2104","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40399489"]},{"id":"https://openalex.org/I4210111989","display_name":"Molsoft (United States)","ror":"https://ror.org/024712k05","country_code":"US","type":"company","lineage":["https://openalex.org/I4210111989"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eugene Raush","raw_affiliation_strings":["1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA"],"affiliations":[{"raw_affiliation_string":"1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I40399489","https://openalex.org/I36258959","https://openalex.org/I4210111989"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064101943","display_name":"Ruben Abagyan","orcid":"https://orcid.org/0000-0001-9309-2976"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I40399489","display_name":"Torrey Pines Institute For Molecular Studies","ror":"https://ror.org/01grq2104","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I40399489"]},{"id":"https://openalex.org/I4210111989","display_name":"Molsoft (United States)","ror":"https://ror.org/024712k05","country_code":"US","type":"company","lineage":["https://openalex.org/I4210111989"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruben Abagyan","raw_affiliation_strings":["1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA"],"affiliations":[{"raw_affiliation_string":"1 UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 and 2Molsoft, LLC, 3366 North Torrey Pines Court, Suite 300, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I40399489","https://openalex.org/I36258959","https://openalex.org/I4210111989"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5023487324"],"corresponding_institution_ids":["https://openalex.org/I36258959","https://openalex.org/I40399489","https://openalex.org/I4210111989"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9488,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.74485956,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"26","issue":"21","first_page":"2784","last_page":"2785"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9990000128746033,"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":0.9983000159263611,"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/computer-science","display_name":"Computer science","score":0.7067702412605286},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.6721507906913757},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6428858041763306},{"id":"https://openalex.org/keywords/web-browser","display_name":"Web browser","score":0.6312322616577148},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6055783033370972},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4930977523326874},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics","score":0.43028366565704346},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4116678833961487},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.387470543384552},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3280711770057678},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.2790016829967499},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.22934585809707642},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.22131305932998657},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08347266912460327}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7067702412605286},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.6721507906913757},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6428858041763306},{"id":"https://openalex.org/C2983909278","wikidata":"https://www.wikidata.org/wiki/Q6368","display_name":"Web browser","level":3,"score":0.6312322616577148},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6055783033370972},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4930977523326874},{"id":"https://openalex.org/C77660652","wikidata":"https://www.wikidata.org/wiki/Q150971","display_name":"Computer graphics","level":2,"score":0.43028366565704346},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4116678833961487},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.387470543384552},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3280711770057678},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.2790016829967499},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.22934585809707642},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.22131305932998657},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08347266912460327},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","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":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":"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":"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btq504","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq504","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/21/2784/564496/btq504.pdf","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:20871105","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20871105","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:pubmedcentral.nih.gov:2981495","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2981495","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq504","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq504","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/21/2784/564496/btq504.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2114599399.pdf","grobid_xml":"https://content.openalex.org/works/W2114599399.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1209932451","https://openalex.org/W1986568494","https://openalex.org/W2021750784","https://openalex.org/W2027638447","https://openalex.org/W2040219737","https://openalex.org/W2058433776","https://openalex.org/W2102110064","https://openalex.org/W2130479394","https://openalex.org/W2137167381","https://openalex.org/W2143482176","https://openalex.org/W2152040212","https://openalex.org/W2166133396","https://openalex.org/W2168045053","https://openalex.org/W2470290884","https://openalex.org/W2791490447"],"related_works":["https://openalex.org/W2294901673","https://openalex.org/W2370647676","https://openalex.org/W2100753372","https://openalex.org/W2221819563","https://openalex.org/W2796425874","https://openalex.org/W2084305201","https://openalex.org/W1987850938","https://openalex.org/W2915362246","https://openalex.org/W2033854691","https://openalex.org/W1844100222"],"abstract_inverted_index":{"SimiCon":[0],"is":[1],"freely":[2],"available":[3],"at":[4],"http://abagyan.ucsd.edu/SimiCon":[5]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"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"}