{"id":"https://openalex.org/W4200613668","doi":"https://doi.org/10.1186/s12859-021-04519-4","title":"pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science","display_name":"pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science","publication_year":2021,"publication_date":"2021-12-01","ids":{"openalex":"https://openalex.org/W4200613668","doi":"https://doi.org/10.1186/s12859-021-04519-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/34930115"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04519-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04519-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04519-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04519-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048144057","display_name":"Jo\u00e3o Victor da Silva Guerra","orcid":"https://orcid.org/0000-0002-6800-4425"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]},{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Jo\u00e3o Victor da Silva Guerra","raw_affiliation_strings":["Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil. joao.guerra@lnbio.cnpem.br","Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, SP, Brazil. joao.guerra@lnbio.cnpem.br","Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil. joao.guerra@lnbio.cnpem.br","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]},{"raw_affiliation_string":"Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, SP, Brazil. joao.guerra@lnbio.cnpem.br","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051059732","display_name":"Helder Veras Ribeiro Filho","orcid":"https://orcid.org/0000-0001-8471-207X"},"institutions":[{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Helder Veras Ribeiro-Filho","raw_affiliation_strings":["Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060155336","display_name":"Gabriel Ernesto Jara","orcid":"https://orcid.org/0000-0002-5831-1392"},"institutions":[{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Gabriel Ernesto Jara","raw_affiliation_strings":["Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054067127","display_name":"Leandro Oliveira Bortot","orcid":"https://orcid.org/0000-0002-0915-8205"},"institutions":[{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Leandro Oliveira Bortot","raw_affiliation_strings":["Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034320215","display_name":"Jos\u00e9 Geraldo de Carvalho Pereira","orcid":"https://orcid.org/0000-0003-1041-0209"},"institutions":[{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Geraldo de Carvalho Pereira","raw_affiliation_strings":["Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065692802","display_name":"Paulo S\u00e9rgio Lopes de Oliveira","orcid":"https://orcid.org/0000-0002-1287-8019"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]},{"id":"https://openalex.org/I4210152696","display_name":"Brazilian Center for Research in Energy and Materials","ror":"https://ror.org/05m235j20","country_code":"BR","type":"other","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696"]},{"id":"https://openalex.org/I4210158387","display_name":"Brazilian Biosciences National Laboratory","ror":"https://ror.org/04kjcjc51","country_code":"BR","type":"facility","lineage":["https://openalex.org/I4210151455","https://openalex.org/I4210152696","https://openalex.org/I4210158387"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Paulo S\u00e9rgio Lopes-de-Oliveira","raw_affiliation_strings":["Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil. paulo.oliveira@lnbio.cnpem.br","Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, SP, Brazil. paulo.oliveira@lnbio.cnpem.br","Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil","Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, SP, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-1287-8019","affiliations":[{"raw_affiliation_string":"Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil. paulo.oliveira@lnbio.cnpem.br","institution_ids":["https://openalex.org/I4210158387"]},{"raw_affiliation_string":"Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, SP, Brazil. paulo.oliveira@lnbio.cnpem.br","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe M\u00e1ximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil","institution_ids":["https://openalex.org/I4210158387","https://openalex.org/I4210152696"]},{"raw_affiliation_string":"Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, SP, Brazil","institution_ids":["https://openalex.org/I181391015"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5048144057"],"corresponding_institution_ids":["https://openalex.org/I181391015","https://openalex.org/I4210152696","https://openalex.org/I4210158387"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.8681,"has_fulltext":true,"cited_by_count":54,"citation_normalized_percentile":{"value":0.84999153,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"22","issue":"1","first_page":"607","last_page":"607"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.4650999903678894,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.4650999903678894,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.2393999993801117,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.02449999935925007,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.8691191673278809},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.7632184624671936},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7456380724906921},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6728472709655762},{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.6078320741653442},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5318692922592163},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.5064977407455444},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4782254099845886},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.4734753370285034},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.33879971504211426},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.33297836780548096},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.30036425590515137},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1910390853881836},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.11373782157897949}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8691191673278809},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.7632184624671936},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7456380724906921},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6728472709655762},{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.6078320741653442},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5318692922592163},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.5064977407455444},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4782254099845886},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.4734753370285034},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.33879971504211426},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.33297836780548096},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30036425590515137},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1910390853881836},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.11373782157897949}],"mesh":[{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077488","descriptor_name":"Data Science","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-021-04519-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04519-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04519-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34930115","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34930115","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:8ed22d93639c46f7a27d48425ed79d7f","is_oa":true,"landing_page_url":"https://doaj.org/article/8ed22d93639c46f7a27d48425ed79d7f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-13 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8685811","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8685811","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04519-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04519-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04519-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3564302848","display_name":null,"funder_award_id":"350244/2020-0","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G7452625484","display_name":null,"funder_award_id":"2018/00629-0","funder_id":"https://openalex.org/F4320320997","funder_display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo"}],"funders":[{"id":"https://openalex.org/F4320320997","display_name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","ror":"https://ror.org/02ddkpn78"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320327334","display_name":"Centro Nacional de Pesquisa em Energia e Materiais","ror":"https://ror.org/05m235j20"},{"id":"https://openalex.org/F4320335750","display_name":"Laborat\u00f3rio Nacional de Bioci\u00eancias","ror":"https://ror.org/04kjcjc51"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4200613668.pdf","grobid_xml":"https://content.openalex.org/works/W4200613668.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1969370763","https://openalex.org/W1975304761","https://openalex.org/W2011301426","https://openalex.org/W2019215286","https://openalex.org/W2019498797","https://openalex.org/W2025859600","https://openalex.org/W2026593599","https://openalex.org/W2031194866","https://openalex.org/W2031901496","https://openalex.org/W2063725620","https://openalex.org/W2066638035","https://openalex.org/W2094889474","https://openalex.org/W2097347921","https://openalex.org/W2105902442","https://openalex.org/W2116703791","https://openalex.org/W2124934990","https://openalex.org/W2131288855","https://openalex.org/W2132395520","https://openalex.org/W2154792548","https://openalex.org/W2164088236","https://openalex.org/W2319902168","https://openalex.org/W2566883605","https://openalex.org/W2742394249","https://openalex.org/W2772099288","https://openalex.org/W2883065891","https://openalex.org/W2898210859","https://openalex.org/W2898364362","https://openalex.org/W2909813131","https://openalex.org/W2972751083","https://openalex.org/W3003257820","https://openalex.org/W3014988774","https://openalex.org/W3021526350","https://openalex.org/W3035965352","https://openalex.org/W3036669765","https://openalex.org/W3043662389","https://openalex.org/W3048429135","https://openalex.org/W3099878876","https://openalex.org/W3103145119","https://openalex.org/W3103588515","https://openalex.org/W3130827974","https://openalex.org/W3165707339","https://openalex.org/W3183475563","https://openalex.org/W6601340852","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W3023169329","https://openalex.org/W4389470870","https://openalex.org/W2782165897","https://openalex.org/W1582950852","https://openalex.org/W4300438041","https://openalex.org/W2054104202","https://openalex.org/W2139703748","https://openalex.org/W2761254753","https://openalex.org/W1024825291","https://openalex.org/W2188981919"],"abstract_inverted_index":{"BACKGROUND:":[0],"Biomolecular":[1],"interactions":[2],"that":[3],"modulate":[4],"biological":[5],"processes":[6],"occur":[7],"mainly":[8],"in":[9,36,73,87,102,131,190,205],"cavities":[10,72,86,189],"throughout":[11],"the":[12,18,27,206],"surface":[13],"of":[14,30,136,147,152],"biomolecular":[15,74,88,188],"structures.":[16,57],"In":[17,42],"data":[19,32,56,77,111,161,191,200,215],"science":[20,78,162,192,216],"era,":[21],"structural":[22,37],"biology":[23],"has":[24],"benefited":[25],"from":[26,106],"increasing":[28],"availability":[29],"biostructural":[31,199],"due":[33],"to":[34,68],"advances":[35],"determination":[38],"and":[39,70,79,90,96,110,121,128,142,149,170,180,186,194,209,217],"computational":[40],"methods.":[41],"this":[43,60],"scenario,":[44],"data-intensive":[45],"cavity":[46,100],"analysis":[47,201],"demands":[48],"efficient":[49],"scripting":[50,203],"routines":[51,204],"built":[52],"on":[53],"easily":[54,181],"manipulated":[55],"To":[58],"fulfill":[59],"need,":[61],"we":[62,139],"developed":[63],"pyKVFinder,":[64,156],"a":[65,150],"Python":[66,107,207],"package":[67],"detect":[69],"characterize":[71],"structures":[75,89],"for":[76,123,184,214],"automated":[80,132,195],"pipelines.":[81],"RESULTS:":[82],"pyKVFinder":[83,113,197],"efficiently":[84],"detects":[85],"computes":[91],"their":[92],"volume,":[93],"area,":[94],"depth":[95],"hydropathy,":[97],"storing":[98],"these":[99],"properties":[101],"NumPy":[103],"arrays.":[104],"Benefited":[105],"ecosystem":[108,208],"interoperability":[109],"structures,":[112],"can":[114,210],"be":[115,211],"integrated":[116],"with":[117,155,160,202],"third-party":[118],"scientific":[119],"packages":[120,163],"libraries":[122],"mathematical":[124],"calculations,":[125],"machine":[126],"learning":[127],"3D":[129],"visualization":[130],"workflows.":[133],"As":[134],"proof":[135],"pyKVFinder's":[137],"capabilities,":[138],"successfully":[140],"identified":[141],"compared":[143],"ADRP":[144],"substrate-binding":[145],"site":[146],"SARS-CoV-2":[148],"set":[151],"homologous":[153],"proteins":[154],"showing":[157],"its":[158],"integrability":[159],"such":[164],"as":[165],"matplotlib,":[166],"NGL":[167],"Viewer,":[168],"SciPy":[169],"Jupyter":[171],"notebook.":[172],"CONCLUSIONS:":[173],"We":[174],"introduce":[175],"an":[176],"efficient,":[177],"highly":[178],"versatile":[179],"integrable":[182],"software":[183],"detecting":[185],"characterizing":[187],"applications":[193],"protocols.":[196],"facilitates":[198],"building":[212],"blocks":[213],"drug":[218],"design":[219],"applications.":[220]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":1}],"updated_date":"2026-06-13T07:54:00.901334","created_date":"2025-10-10T00:00:00"}
