{"id":"https://openalex.org/W2799327292","doi":"https://doi.org/10.1093/nar/gky380","title":"CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction","display_name":"CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction","publication_year":2018,"publication_date":"2018-04-30","ids":{"openalex":"https://openalex.org/W2799327292","doi":"https://doi.org/10.1093/nar/gky380","mag":"2799327292","pmid":"https://pubmed.ncbi.nlm.nih.gov/29750256"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gky380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gky380","pdf_url":"https://academic.oup.com/nar/article-pdf/46/W1/W374/25110156/gky380.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":null,"license_id":null,"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/46/W1/W374/25110156/gky380.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004269850","display_name":"Youjun Xu","orcid":"https://orcid.org/0000-0002-3086-9781"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Youjun Xu","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100340291","display_name":"Shiwei Wang","orcid":"https://orcid.org/0000-0003-2175-1156"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiwei Wang","raw_affiliation_strings":["School of Life Sciences, Peking University, Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Sciences, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002949317","display_name":"Qiwan Hu","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiwan Hu","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087526123","display_name":"Shuaishi Gao","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuaishi Gao","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057719232","display_name":"Xiaomin Ma","orcid":"https://orcid.org/0009-0006-0458-5132"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaomin Ma","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100680395","display_name":"Weilin Zhang","orcid":"https://orcid.org/0000-0002-2774-0944"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210116048","display_name":"Beijing National Laboratory for Molecular Sciences","ror":"https://ror.org/02601yx74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210116048"]},{"id":"https://openalex.org/I4391768210","display_name":"State Key Laboratory for Structural Chemistry of Unstable and Stable Species","ror":"https://ror.org/03mw4pt79","country_code":null,"type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210155088","https://openalex.org/I4391768210"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weilin Zhang","raw_affiliation_strings":["BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China","Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I4210116048","https://openalex.org/I20231570","https://openalex.org/I4391768210"]},{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083540149","display_name":"Yihang Shen","orcid":"https://orcid.org/0000-0002-6161-3906"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210116048","display_name":"Beijing National Laboratory for Molecular Sciences","ror":"https://ror.org/02601yx74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210116048"]},{"id":"https://openalex.org/I4391768210","display_name":"State Key Laboratory for Structural Chemistry of Unstable and Stable Species","ror":"https://ror.org/03mw4pt79","country_code":null,"type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210155088","https://openalex.org/I4391768210"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yihang Shen","raw_affiliation_strings":["BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I4210116048","https://openalex.org/I20231570","https://openalex.org/I4391768210"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081235048","display_name":"Fangjin Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fangjin Chen","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064049271","display_name":"Luhua Lai","orcid":"https://orcid.org/0000-0002-8343-7587"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210116048","display_name":"Beijing National Laboratory for Molecular Sciences","ror":"https://ror.org/02601yx74","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210116048"]},{"id":"https://openalex.org/I4391768210","display_name":"State Key Laboratory for Structural Chemistry of Unstable and Stable Species","ror":"https://ror.org/03mw4pt79","country_code":null,"type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210155088","https://openalex.org/I4391768210"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Luhua Lai","raw_affiliation_strings":["BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China","Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China","institution_ids":["https://openalex.org/I4210116048","https://openalex.org/I20231570","https://openalex.org/I4391768210"]},{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047704083","display_name":"Jianfeng Pei","orcid":"https://orcid.org/0000-0002-8482-1185"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianfeng Pei","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing\u00a0100871, China","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5047704083","https://openalex.org/A5064049271"],"corresponding_institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210116048","https://openalex.org/I4391768210"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":18.9344,"has_fulltext":false,"cited_by_count":380,"citation_normalized_percentile":{"value":0.99531067,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"46","issue":"W1","first_page":"W374","last_page":"W379"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"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":0.9995999932289124,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.9976000189781189,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/druggability","display_name":"Druggability","score":0.9352514147758484},{"id":"https://openalex.org/keywords/pharmacophore","display_name":"Pharmacophore","score":0.9348419904708862},{"id":"https://openalex.org/keywords/allosteric-regulation","display_name":"Allosteric regulation","score":0.8860690593719482},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.7129558324813843},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6836853623390198},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5887147784233093},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5684576630592346},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.557873547077179},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.552349865436554},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5489131808280945},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.48226624727249146},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3448585271835327},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.266487181186676},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.26604801416397095},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.1355360746383667},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.106438547372818},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.08243528008460999}],"concepts":[{"id":"https://openalex.org/C10679952","wikidata":"https://www.wikidata.org/wiki/Q5308937","display_name":"Druggability","level":3,"score":0.9352514147758484},{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.9348419904708862},{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.8860690593719482},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.7129558324813843},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6836853623390198},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5887147784233093},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5684576630592346},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.557873547077179},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.552349865436554},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5489131808280945},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.48226624727249146},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3448585271835327},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.266487181186676},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.26604801416397095},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.1355360746383667},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.106438547372818},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.08243528008460999},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000495","descriptor_name":"Allosteric Site","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":true},{"descriptor_ui":"D055592","descriptor_name":"Biophysical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055592","descriptor_name":"Biophysical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055592","descriptor_name":"Biophysical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gky380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gky380","pdf_url":"https://academic.oup.com/nar/article-pdf/46/W1/W374/25110156/gky380.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:29750256","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29750256","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:europepmc.org:4991327","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6031032","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gky380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gky380","pdf_url":"https://academic.oup.com/nar/article-pdf/46/W1/W374/25110156/gky380.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":null,"license_id":null,"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/G2721886344","display_name":null,"funder_award_id":"2015CB910302","funder_id":"https://openalex.org/F4320321540","funder_display_name":"Ministry of Science and Technology of the People's Republic of China"},{"id":"https://openalex.org/G2815554813","display_name":null,"funder_award_id":"21673010","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3761634645","display_name":"\u86cb\u767d\u8d28\u522b\u6784\u8c03\u63a7\u673a\u5236\u7814\u7a76","funder_award_id":"21633001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6814657793","display_name":null,"funder_award_id":"2016YFA05023032","funder_id":"https://openalex.org/F4320321540","funder_display_name":"Ministry of Science and Technology of the People's Republic of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321160","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71"},{"id":"https://openalex.org/F4320321540","display_name":"Ministry of Science and Technology of the People's Republic of China","ror":"https://ror.org/027s68j25"},{"id":"https://openalex.org/F4320321657","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377"},{"id":"https://openalex.org/F4320326860","display_name":"East China Institute of Technology","ror":"https://ror.org/027385r44"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1522872937","https://openalex.org/W1978509310","https://openalex.org/W1991445257","https://openalex.org/W1992041755","https://openalex.org/W1993046136","https://openalex.org/W2009212164","https://openalex.org/W2010993054","https://openalex.org/W2011703027","https://openalex.org/W2018339027","https://openalex.org/W2019792957","https://openalex.org/W2025135899","https://openalex.org/W2041205020","https://openalex.org/W2041664602","https://openalex.org/W2065708060","https://openalex.org/W2073746700","https://openalex.org/W2074929227","https://openalex.org/W2076790509","https://openalex.org/W2091708007","https://openalex.org/W2092285329","https://openalex.org/W2094295896","https://openalex.org/W2108700551","https://openalex.org/W2117888214","https://openalex.org/W2128716813","https://openalex.org/W2167854315","https://openalex.org/W2175309784","https://openalex.org/W2208203352","https://openalex.org/W2211224366","https://openalex.org/W2294442692","https://openalex.org/W2512708954","https://openalex.org/W2615598191","https://openalex.org/W6631148520"],"related_works":["https://openalex.org/W2000397010","https://openalex.org/W2115078847","https://openalex.org/W2062768126","https://openalex.org/W1971603507","https://openalex.org/W2969563261","https://openalex.org/W2061401330","https://openalex.org/W2055137136","https://openalex.org/W3041915240","https://openalex.org/W2077097504","https://openalex.org/W2586171341"],"abstract_inverted_index":{"CavityPlus":[0,22,111,154],"is":[1,97,157],"a":[2,34,64],"web":[3,155],"server":[4,156],"that":[5],"offers":[6],"protein":[7,15,36,121],"cavity":[8],"detection":[9],"and":[10,38,44,60,134,139,147,149],"various":[11],"functional":[12],"analyses.":[13],"Using":[14],"three-dimensional":[16],"structural":[17],"information":[18],"as":[19],"the":[20,31],"input,":[21],"applies":[23],"CAVITY":[24],"to":[25,70,100],"detect":[26],"potential":[27,48,79],"binding":[28,49,103,122],"sites":[29,50,82,104],"on":[30,42,84],"surface":[32],"of":[33,120,131],"given":[35],"structure":[37],"rank":[39],"them":[40],"based":[41,83],"ligandability":[43],"druggability":[45],"scores.":[46],"These":[47],"can":[51],"be":[52],"further":[53],"analysed":[54],"using":[55],"three":[56],"submodules,":[57],"CavPharmer,":[58],"CorrSite,":[59],"CovCys.":[61],"CavPharmer":[62],"uses":[63],"receptor-based":[65],"pharmacophore":[66,73],"modelling":[67],"program,":[68],"Pocket,":[69],"automatically":[71,91],"extract":[72],"features":[74],"within":[75],"cavities.":[76,89,123],"CorrSite":[77],"identifies":[78],"allosteric":[80,108,148],"ligand-binding":[81],"motion":[85],"correlation":[86],"analyses":[87,125],"between":[88],"CovCys":[90],"detects":[92],"druggable":[93],"cysteine":[94],"residues,":[95],"which":[96],"especially":[98],"useful":[99,127],"identify":[101],"novel":[102],"for":[105,116,128],"designing":[106],"covalent":[107],"ligands.":[109],"Overall,":[110],"provides":[112],"an":[113],"integrated":[114],"platform":[115],"analysing":[117],"comprehensive":[118],"properties":[119],"Such":[124],"are":[126],"many":[129],"aspects":[130],"drug":[132,145,151],"design":[133],"discovery,":[135],"including":[136],"target":[137],"selection":[138],"identification,":[140],"virtual":[141],"screening,":[142],"de":[143],"novo":[144],"design,":[146],"covalent-binding":[150],"design.":[152],"The":[153],"freely":[158],"available":[159],"at":[160],"http://repharma.pku.edu.cn/cavityplus":[161],"or":[162],"http://www.pkumdl.cn/cavityplus.":[163]},"counts_by_year":[{"year":2026,"cited_by_count":32},{"year":2025,"cited_by_count":75},{"year":2024,"cited_by_count":51},{"year":2023,"cited_by_count":60},{"year":2022,"cited_by_count":61},{"year":2021,"cited_by_count":47},{"year":2020,"cited_by_count":34},{"year":2019,"cited_by_count":16},{"year":2018,"cited_by_count":3}],"updated_date":"2026-07-16T13:24:37.021932","created_date":"2025-10-10T00:00:00"}