{"id":"https://openalex.org/W2017422947","doi":"https://doi.org/10.1007/s10822-010-9402-0","title":"Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction","display_name":"Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction","publication_year":2010,"publication_date":"2010-11-20","ids":{"openalex":"https://openalex.org/W2017422947","doi":"https://doi.org/10.1007/s10822-010-9402-0","mag":"2017422947","pmid":"https://pubmed.ncbi.nlm.nih.gov/21104192"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-010-9402-0","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-010-9402-0","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-010-9402-0.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"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":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10822-010-9402-0.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110162129","display_name":"Katarzyna Prymula","orcid":null},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Katarzyna Prymula","raw_affiliation_strings":["Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland. prymula@chemia.uj.edu.pl","Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060, Krakow, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland. prymula@chemia.uj.edu.pl","institution_ids":["https://openalex.org/I126596746"]},{"raw_affiliation_string":"Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060, Krakow, Poland","institution_ids":["https://openalex.org/I126596746"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045987075","display_name":"Tomasz Jadczyk","orcid":"https://orcid.org/0000-0002-7955-9100"},"institutions":[{"id":"https://openalex.org/I686019","display_name":"AGH University of Krakow","ror":"https://ror.org/00bas1c41","country_code":"PL","type":"education","lineage":["https://openalex.org/I686019"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Tomasz Jadczyk","raw_affiliation_strings":["Department of Electronics, AGH University of Science and Technology, 30 Mickiewicza Avenue, 30-059, Krakow, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electronics, AGH University of Science and Technology, 30 Mickiewicza Avenue, 30-059, Krakow, Poland","institution_ids":["https://openalex.org/I686019"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087239926","display_name":"Irena Roterman","orcid":"https://orcid.org/0000-0003-3652-9099"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Irena Roterman","raw_affiliation_strings":["Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, 16 Lazarza Street, 31-530, Krakow, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, 16 Lazarza Street, 31-530, Krakow, Poland","institution_ids":["https://openalex.org/I126596746"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5110162129"],"corresponding_institution_ids":["https://openalex.org/I126596746"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":{"value":2890,"currency":"EUR","value_usd":3690},"fwci":5.1533,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.95526141,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"25","issue":"2","first_page":"117","last_page":"133"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9980999827384949,"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":0.9980999827384949,"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":0.9966999888420105,"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":0.9948999881744385,"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/convex-hull","display_name":"Convex hull","score":0.4811905026435852},{"id":"https://openalex.org/keywords/accessible-surface-area","display_name":"Accessible surface area","score":0.4683460593223572},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46263307332992554},{"id":"https://openalex.org/keywords/active-site","display_name":"Active site","score":0.4574342370033264},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.35299986600875854},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.33680444955825806},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2643270492553711},{"id":"https://openalex.org/keywords/catalysis","display_name":"Catalysis","score":0.26139408349990845},{"id":"https://openalex.org/keywords/regular-polygon","display_name":"Regular polygon","score":0.23232987523078918},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.14246532320976257},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.1171136200428009},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08392584323883057}],"concepts":[{"id":"https://openalex.org/C206194317","wikidata":"https://www.wikidata.org/wiki/Q1138624","display_name":"Convex hull","level":3,"score":0.4811905026435852},{"id":"https://openalex.org/C11072593","wikidata":"https://www.wikidata.org/wiki/Q3622068","display_name":"Accessible surface area","level":2,"score":0.4683460593223572},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46263307332992554},{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.4574342370033264},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.35299986600875854},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.33680444955825806},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2643270492553711},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.26139408349990845},{"id":"https://openalex.org/C112680207","wikidata":"https://www.wikidata.org/wiki/Q714886","display_name":"Regular polygon","level":2,"score":0.23232987523078918},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.14246532320976257},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.1171136200428009},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08392584323883057},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"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":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020134","descriptor_name":"Catalytic Domain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020836","descriptor_name":"Protein Structure, Quaternary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020836","descriptor_name":"Protein Structure, Quaternary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020836","descriptor_name":"Protein Structure, Quaternary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1007/s10822-010-9402-0","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-010-9402-0","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-010-9402-0.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"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":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:21104192","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21104192","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 computer-aided molecular design","raw_type":null},{"id":"pmh:oai:ruj.uj.edu.pl:item/71080","is_oa":true,"landing_page_url":"https://ruj.uj.edu.pl/xmlui/handle/item/71080","pdf_url":"http://ruj.uj.edu.pl/bitstreams/c152dcfe-cd5c-4e9c-b176-ff6de4d56219/download","source":{"id":"https://openalex.org/S4306401249","display_name":"Jagiellonian University Repository (Jagiellonian University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I126596746","host_organization_name":"Jagiellonian University","host_organization_lineage":["https://openalex.org/I126596746"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3032897","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3032897","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":"J Comput Aided Mol Des","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s10822-010-9402-0","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-010-9402-0","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-010-9402-0.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"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":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2017422947.pdf","grobid_xml":"https://content.openalex.org/works/W2017422947.grobid-xml"},"referenced_works_count":108,"referenced_works":["https://openalex.org/W43803018","https://openalex.org/W196131166","https://openalex.org/W1482591743","https://openalex.org/W1496844582","https://openalex.org/W1517566065","https://openalex.org/W1571577887","https://openalex.org/W1614421135","https://openalex.org/W1633146128","https://openalex.org/W1758070551","https://openalex.org/W1964640688","https://openalex.org/W1965091809","https://openalex.org/W1968733906","https://openalex.org/W1969456631","https://openalex.org/W1969888071","https://openalex.org/W1977845138","https://openalex.org/W1979598348","https://openalex.org/W1979914800","https://openalex.org/W1985203726","https://openalex.org/W1986154009","https://openalex.org/W1986969007","https://openalex.org/W1990369574","https://openalex.org/W1990598130","https://openalex.org/W1999032243","https://openalex.org/W1999319994","https://openalex.org/W2000621476","https://openalex.org/W2003165115","https://openalex.org/W2004360551","https://openalex.org/W2006011269","https://openalex.org/W2008708467","https://openalex.org/W2009297402","https://openalex.org/W2013600324","https://openalex.org/W2021954541","https://openalex.org/W2025088751","https://openalex.org/W2027036222","https://openalex.org/W2031194866","https://openalex.org/W2035353430","https://openalex.org/W2043886357","https://openalex.org/W2043904638","https://openalex.org/W2045110975","https://openalex.org/W2046977075","https://openalex.org/W2047544230","https://openalex.org/W2048205675","https://openalex.org/W2049476058","https://openalex.org/W2052666367","https://openalex.org/W2058463742","https://openalex.org/W2059067075","https://openalex.org/W2066143642","https://openalex.org/W2069663555","https://openalex.org/W2070196801","https://openalex.org/W2077776336","https://openalex.org/W2077847478","https://openalex.org/W2082972649","https://openalex.org/W2084426324","https://openalex.org/W2088534163","https://openalex.org/W2091563009","https://openalex.org/W2094833702","https://openalex.org/W2095943622","https://openalex.org/W2096039340","https://openalex.org/W2096942889","https://openalex.org/W2098151554","https://openalex.org/W2098473889","https://openalex.org/W2099389777","https://openalex.org/W2100494857","https://openalex.org/W2101449937","https://openalex.org/W2102333330","https://openalex.org/W2105902442","https://openalex.org/W2107432340","https://openalex.org/W2108067237","https://openalex.org/W2108302275","https://openalex.org/W2112109058","https://openalex.org/W2113024639","https://openalex.org/W2113944588","https://openalex.org/W2114441129","https://openalex.org/W2114782816","https://openalex.org/W2115230913","https://openalex.org/W2116435022","https://openalex.org/W2116973522","https://openalex.org/W2117135374","https://openalex.org/W2117164735","https://openalex.org/W2119087770","https://openalex.org/W2119498937","https://openalex.org/W2123060905","https://openalex.org/W2127670503","https://openalex.org/W2128402268","https://openalex.org/W2129695675","https://openalex.org/W2134952459","https://openalex.org/W2135661937","https://openalex.org/W2136255360","https://openalex.org/W2137991504","https://openalex.org/W2139942857","https://openalex.org/W2142757818","https://openalex.org/W2144714500","https://openalex.org/W2151345203","https://openalex.org/W2154333184","https://openalex.org/W2156575953","https://openalex.org/W2156728093","https://openalex.org/W2157236640","https://openalex.org/W2158698691","https://openalex.org/W2161062388","https://openalex.org/W2163352757","https://openalex.org/W2165181282","https://openalex.org/W2166211977","https://openalex.org/W2170968124","https://openalex.org/W2171970785","https://openalex.org/W2172063092","https://openalex.org/W2430084315","https://openalex.org/W4211083314","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W2607424097","https://openalex.org/W2606230654","https://openalex.org/W2319480705","https://openalex.org/W2398689458"],"abstract_inverted_index":{"The":[0,12,35,53,65,93,153],"comparison":[1],"of":[2,18,37,63,79,96,106,112,129,136,144],"eight":[3,131],"tools":[4],"applicable":[5],"to":[6,43,71,141],"ligand-binding":[7],"site":[8,149],"prediction":[9,150],"is":[10,151,171],"presented.":[11,134],"methods":[13,109,132],"examined":[14],"cover":[15],"three":[16],"types":[17],"approaches:":[19],"the":[20,25,30,44,49,101,107,113,118,130,142,147,161,172,176],"geometrical":[21,177],"(CASTp,":[22],"PASS,":[23],"Pocket-Finder),":[24],"physicochemical":[26],"(Q-SiteFinder,":[27],"FOD)":[28],"and":[29,127],"knowledge-based":[31],"(ConSurf,":[32],"SuMo,":[33],"WebFEATURE).":[34],"accuracy":[36],"predictions":[38,97],"was":[39,55,123],"measured":[40],"in":[41,48,88,100,139,146],"reference":[42],"catalytic":[45],"residues":[46],"documented":[47],"Catalytic":[50],"Site":[51],"Atlas.":[52],"test":[54],"performed":[56],"on":[57],"a":[58],"set":[59],"comprising":[60],"selected":[61],"chains":[62,138],"hydrolases.":[64],"results":[66],"were":[67],"analysed":[68],"with":[69],"regard":[70],"size,":[72],"polarity,":[73],"secondary":[74],"structure,":[75],"accessible":[76],"solvent":[77],"area":[78],"predicted":[80],"sites":[81],"as":[82,84],"well":[83],"parameters":[85],"commonly":[86],"used":[87],"machine":[89],"learning":[90],"(F-measure,":[91],"MCC).":[92],"relative":[94],"accuracies":[95],"are":[98,133,158],"presented":[99],"ROC":[102,114],"space,":[103],"allowing":[104],"determination":[105],"optimal":[108],"by":[110,167],"means":[111],"convex":[115],"hull.":[116],"Additionally":[117],"minimum":[119],"expected":[120],"cost":[121],"analysis":[122],"performed.":[124],"Both":[125],"advantages":[126],"disadvantages":[128],"Characterization":[135],"protein":[137],"respect":[140],"level":[143],"difficulty":[145],"active":[148],"introduced.":[152],"main":[154],"reasons":[155],"for":[156],"failures":[157],"discussed.":[159],"Overall,":[160],"best":[162,173],"performance":[163],"offers":[164],"SuMo":[165],"followed":[166],"FOD,":[168],"while":[169],"Pocket-Finder":[170],"method":[174],"among":[175],"approaches.":[178]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":6}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}
