{"id":"https://openalex.org/W2059981954","doi":"https://doi.org/10.1371/journal.pcbi.1003829","title":"eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models","display_name":"eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models","publication_year":2014,"publication_date":"2014-09-18","ids":{"openalex":"https://openalex.org/W2059981954","doi":"https://doi.org/10.1371/journal.pcbi.1003829","mag":"2059981954","pmid":"https://pubmed.ncbi.nlm.nih.gov/25232727"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003829","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003829","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003829&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003829&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033579800","display_name":"Micha\u0142 Bryli\u0144ski","orcid":"https://orcid.org/0000-0002-6204-2869"},"institutions":[{"id":"https://openalex.org/I121820613","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57","country_code":"US","type":"education","lineage":["https://openalex.org/I121820613"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michal Brylinski","raw_affiliation_strings":["Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America; Center for Computation & Technology, Louisiana State University, Baton Rouge, Louisiana, United States of America","Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America","Center for Computation & Technology, Louisiana State University, Baton Rouge, Louisiana, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America; Center for Computation & Technology, Louisiana State University, Baton Rouge, Louisiana, United States of America","institution_ids":[]},{"raw_affiliation_string":"Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America","institution_ids":["https://openalex.org/I121820613"]},{"raw_affiliation_string":"Center for Computation & Technology, Louisiana State University, Baton Rouge, Louisiana, United States of America","institution_ids":["https://openalex.org/I121820613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5033579800"],"corresponding_institution_ids":["https://openalex.org/I121820613"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.4261,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.81047698,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"9","first_page":"e1003829","last_page":"e1003829"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983999729156494,"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":0.9983999729156494,"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":0.9983999729156494,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9958000183105469,"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/computational-biology","display_name":"Computational biology","score":0.6068095564842224},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5838631987571716},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.5660346746444702},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5109738111495972},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.49045655131340027},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.4890161454677582},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4882500469684601},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4808862507343292},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.46518629789352417},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.44371387362480164},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.4387335479259491},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.43216049671173096},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3503018021583557},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.331551194190979},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31985723972320557},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1735873520374298},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14220619201660156},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13971608877182007},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.09203410148620605}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6068095564842224},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5838631987571716},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.5660346746444702},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5109738111495972},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.49045655131340027},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.4890161454677582},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4882500469684601},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4808862507343292},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.46518629789352417},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44371387362480164},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.4387335479259491},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.43216049671173096},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3503018021583557},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.331551194190979},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31985723972320557},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1735873520374298},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14220619201660156},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13971608877182007},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.09203410148620605},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","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},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1003829","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003829","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003829&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:25232727","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25232727","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:digitalcommons.lsu.edu:biosci_pubs-1648","is_oa":false,"landing_page_url":"https://digitalcommons.lsu.edu/biosci_pubs/649","pdf_url":null,"source":{"id":"https://openalex.org/S4210169993","display_name":"Civil War Book Review","issn_l":"1528-6592","issn":["1528-6592"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310315936","host_organization_name":"Louisiana State University","host_organization_lineage":["https://openalex.org/P4310315936"],"host_organization_lineage_names":["Louisiana State University"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.787.1100","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.787.1100","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/7a/80/pcbi.1003829.PMC4168975.pdf","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1003829","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003829","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:1ab53cdfcdf3459ca73ccbefbadcfbce","is_oa":true,"landing_page_url":"https://doaj.org/article/1ab53cdfcdf3459ca73ccbefbadcfbce","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 10, Iss 9, p e1003829 (2014)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/1174452","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_e_MatchSite_Sequence_Order_Independent_Structure_Alignments_of_Ligand_Binding_Pockets_in_Protein_Models/1174452","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:4168975","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4168975","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:repository.lsu.edu:biosci_pubs-1648","is_oa":false,"landing_page_url":"https://repository.lsu.edu/biosci_pubs/649","pdf_url":null,"source":{"id":"https://openalex.org/S4210169993","display_name":"Civil War Book Review","issn_l":"1528-6592","issn":["1528-6592"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/P4310315936","host_organization_name":"Louisiana State University","host_organization_lineage":["https://openalex.org/P4310315936"],"host_organization_lineage_names":["Louisiana State University"],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003829","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003829","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003829&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1095431967","display_name":null,"funder_award_id":"LEQSF(2012-15)-RD-A-05","funder_id":"https://openalex.org/F4320309392","funder_display_name":"Louisiana Board of Regents"}],"funders":[{"id":"https://openalex.org/F4320309392","display_name":"Louisiana Board of Regents","ror":"https://ror.org/00jv89z46"},{"id":"https://openalex.org/F4320310395","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2059981954.pdf","grobid_xml":"https://content.openalex.org/works/W2059981954.grobid-xml"},"referenced_works_count":82,"referenced_works":["https://openalex.org/W65846014","https://openalex.org/W1515975222","https://openalex.org/W1963523582","https://openalex.org/W1969657447","https://openalex.org/W1972821149","https://openalex.org/W1974638435","https://openalex.org/W1975017420","https://openalex.org/W1975304761","https://openalex.org/W1975447903","https://openalex.org/W1979453000","https://openalex.org/W1981316712","https://openalex.org/W1982309045","https://openalex.org/W1984501109","https://openalex.org/W1984547849","https://openalex.org/W1984627852","https://openalex.org/W1993568862","https://openalex.org/W1993689973","https://openalex.org/W1995875735","https://openalex.org/W1997037174","https://openalex.org/W2003932708","https://openalex.org/W2015147525","https://openalex.org/W2021954541","https://openalex.org/W2023400093","https://openalex.org/W2024908724","https://openalex.org/W2026582002","https://openalex.org/W2031194866","https://openalex.org/W2040595595","https://openalex.org/W2041848124","https://openalex.org/W2053418558","https://openalex.org/W2055140399","https://openalex.org/W2056530947","https://openalex.org/W2067852761","https://openalex.org/W2068997255","https://openalex.org/W2074231493","https://openalex.org/W2074370114","https://openalex.org/W2079639517","https://openalex.org/W2083589318","https://openalex.org/W2085277871","https://openalex.org/W2085398335","https://openalex.org/W2085833518","https://openalex.org/W2091950883","https://openalex.org/W2094108392","https://openalex.org/W2095400606","https://openalex.org/W2096039340","https://openalex.org/W2103935383","https://openalex.org/W2104133425","https://openalex.org/W2107903949","https://openalex.org/W2108617847","https://openalex.org/W2112878061","https://openalex.org/W2117164735","https://openalex.org/W2121429516","https://openalex.org/W2121604817","https://openalex.org/W2127067710","https://openalex.org/W2128397296","https://openalex.org/W2129697991","https://openalex.org/W2130479394","https://openalex.org/W2131322954","https://openalex.org/W2133035849","https://openalex.org/W2135085917","https://openalex.org/W2138010103","https://openalex.org/W2138770756","https://openalex.org/W2141461755","https://openalex.org/W2142598588","https://openalex.org/W2143000571","https://openalex.org/W2144258433","https://openalex.org/W2144357990","https://openalex.org/W2146940292","https://openalex.org/W2149775989","https://openalex.org/W2150065588","https://openalex.org/W2153187042","https://openalex.org/W2153635508","https://openalex.org/W2158714788","https://openalex.org/W2161151688","https://openalex.org/W2162011385","https://openalex.org/W2162052906","https://openalex.org/W2189421927","https://openalex.org/W2222512263","https://openalex.org/W2314111724","https://openalex.org/W2322154235","https://openalex.org/W2949243165","https://openalex.org/W3182520187","https://openalex.org/W4230932396"],"related_works":["https://openalex.org/W4206949911","https://openalex.org/W3171039768","https://openalex.org/W2253761889","https://openalex.org/W3016550772","https://openalex.org/W107329556","https://openalex.org/W3204091482","https://openalex.org/W2380350064","https://openalex.org/W2593264178","https://openalex.org/W2185518315","https://openalex.org/W1987474460"],"abstract_inverted_index":{"Detecting":[0],"similarities":[1],"between":[2,12],"ligand":[3,100,141,213],"binding":[4,29,49,101,142,189,214],"sites":[5,102,157,190,215],"in":[6,58,64,103,112,140,144,158,186,216,235],"the":[7,21,59,79,86,149,182,221,246],"absence":[8],"of":[9,20,24,81,99,151,155,184,198],"global":[10],"homology":[11],"target":[13],"proteins":[14],"has":[15],"been":[16],"recognized":[17],"as":[18,249],"one":[19],"critical":[22],"components":[23],"modern":[25],"drug":[26,239],"discovery.":[27],"Local":[28],"site":[30,50],"alignments":[31,98,120,210],"can":[32],"be":[33],"constructed":[34],"using":[35,109,170,200,211],"sequence":[36,96],"order-independent":[37,97],"techniques,":[38],"however,":[39],"to":[40,137,223,245],"achieve":[41],"a":[42,91,134,175,250,253],"high":[43,135],"accuracy,":[44],"many":[45],"current":[46],"algorithms":[47],"for":[48,78,94,121,228],"comparison":[51],"require":[52],"high-quality":[53],"experimental":[54],"protein":[55,104,126,145,161,204,217],"structures,":[56],"preferably":[57],"bound":[60],"conformational":[61],"state.":[62],"This,":[63],"turn,":[65],"complicates":[66],"proteome":[67],"scale":[68],"applications,":[69],"where":[70],"only":[71,164],"various":[72],"quality":[73],"structure":[74],"models":[75,162,218],"are":[76],"available":[77,244],"majority":[80],"gene":[82],"products.":[83],"To":[84],"improve":[85],"state-of-the-art,":[87],"we":[88],"developed":[89],"eMatchSite,":[90],"new":[92],"method":[93],"constructing":[95],"models.":[105,146],"Large-scale":[106],"benchmarking":[107],"calculations":[108],"adenine-binding":[110,156],"pockets":[111],"crystal":[113,171],"structures":[114],"demonstrate":[115],"that":[116,197],"eMatchSite":[117,132,185,241],"generates":[118],"accurate":[119],"almost":[122],"three":[123],"times":[124],"more":[125],"pairs":[127,154],"than":[128,167,196],"SOIPPA.":[129],"More":[130],"importantly,":[131],"offers":[133],"tolerance":[136],"structural":[138],"distortions":[139],"regions":[143],"For":[147],"example,":[148],"percentage":[150],"correctly":[152],"aligned":[153,169],"weakly":[159],"homologous":[160],"is":[163,191,242],"4-9%":[165],"lower":[166],"those":[168],"structures.":[172],"This":[173],"represents":[174],"significant":[176],"improvement":[177],"over":[178],"other":[179],"algorithms,":[180],"e.g.":[181],"performance":[183],"recognizing":[187],"similar":[188],"6%":[192],"and":[193,202,237,252],"13%":[194],"higher":[195],"SiteEngine":[199],"high-":[201],"moderate-quality":[203],"models,":[205],"respectively.":[206],"Constructing":[207],"biologically":[208],"correct":[209],"predicted":[212],"opens":[219],"up":[220],"possibility":[222],"investigate":[224],"drug-protein":[225],"interaction":[226],"networks":[227],"complete":[229],"proteomes":[230],"with":[231],"prospective":[232],"systems-level":[233],"applications":[234],"polypharmacology":[236],"rational":[238],"repositioning.":[240],"freely":[243],"academic":[247],"community":[248],"web-server":[251],"stand-alone":[254],"software":[255],"distribution":[256],"at":[257],"http://www.brylinski.org/ematchsite.":[258]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
