{"id":"https://openalex.org/W2019498797","doi":"https://doi.org/10.1186/1471-2105-15-197","title":"KVFinder: steered identification of protein cavities as a PyMOL plugin","display_name":"KVFinder: steered identification of protein cavities as a PyMOL plugin","publication_year":2014,"publication_date":"2014-06-17","ids":{"openalex":"https://openalex.org/W2019498797","doi":"https://doi.org/10.1186/1471-2105-15-197","mag":"2019498797","pmid":"https://pubmed.ncbi.nlm.nih.gov/24938294"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-197","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-197","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-197","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/counter/pdf/10.1186/1471-2105-15-197","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113785362","display_name":"Saulo Henrique Pires de Oliveira","orcid":null},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210146357","display_name":"Oxford BioMedica (United Kingdom)","ror":"https://ror.org/03dp0vf82","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210146357"]}],"countries":["BR","GB"],"is_corresponding":false,"raw_author_name":"Saulo HP Oliveira","raw_affiliation_strings":["Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, 1010 IME-USP, Bloco B, sala 137, CEP 05508-050, S\u00e3o Paulo, Brazil","System Approaches to Biomedical Sciences Industrial Doctorate Centre - Doctoral Training Centre, University of Oxford, 127, Magdalen Road, Postal code OX4 1RJ, Oxford, UK","System Approaches to Biomedical Sciences Industrial Doctorate Centre - Doctoral Training Centre, University of Oxford, Oxford, UK","Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, S\u00e3o Paulo, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, 1010 IME-USP, Bloco B, sala 137, CEP 05508-050, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I17974374"]},{"raw_affiliation_string":"System Approaches to Biomedical Sciences Industrial Doctorate Centre - Doctoral Training Centre, University of Oxford, 127, Magdalen Road, Postal code OX4 1RJ, Oxford, UK","institution_ids":["https://openalex.org/I4210146357"]},{"raw_affiliation_string":"System Approaches to Biomedical Sciences Industrial Doctorate Centre - Doctoral Training Centre, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I17974374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013378133","display_name":"Felipe A. N. Ferraz","orcid":null},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]},{"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":"Felipe AN Ferraz","raw_affiliation_strings":["Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, 1010 IME-USP, Bloco B, sala 137, CEP 05508-050, S\u00e3o Paulo, Brazil","National Laboratory of Biosciences, P.O. Box 6192, CEP 13083-970, Campinas, SP, Brazil","Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, S\u00e3o Paulo, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, 1010 IME-USP, Bloco B, sala 137, CEP 05508-050, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I17974374"]},{"raw_affiliation_string":"National Laboratory of Biosciences, P.O. Box 6192, CEP 13083-970, Campinas, SP, Brazil","institution_ids":["https://openalex.org/I4210158387"]},{"raw_affiliation_string":"Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I17974374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073057216","display_name":"Rodrigo V. Honorato","orcid":"https://orcid.org/0000-0001-5267-3002"},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]},{"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":"Rodrigo V Honorato","raw_affiliation_strings":["Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, 1010 IME-USP, Bloco B, sala 137, CEP 05508-050, S\u00e3o Paulo, Brazil","National Laboratory of Biosciences, P.O. Box 6192, CEP 13083-970, Campinas, SP, Brazil","Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, S\u00e3o Paulo, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, 1010 IME-USP, Bloco B, sala 137, CEP 05508-050, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I17974374"]},{"raw_affiliation_string":"National Laboratory of Biosciences, P.O. Box 6192, CEP 13083-970, Campinas, SP, Brazil","institution_ids":["https://openalex.org/I4210158387"]},{"raw_affiliation_string":"Inter-institutional Grad Program on Bioinformatics, University of S\u00e3o Paulo, Rua do Mat\u00e3o, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I17974374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032826039","display_name":"Jos\u00e9 Xavier\u2010Neto","orcid":"https://orcid.org/0000-0003-4648-789X"},"institutions":[{"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 Xavier-Neto","raw_affiliation_strings":["National Laboratory of Biosciences, P.O. Box 6192, CEP 13083-970, Campinas, SP, Brazil","National Laboratory of Biosciences, Campinas, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Laboratory of Biosciences, P.O. Box 6192, CEP 13083-970, Campinas, SP, Brazil","institution_ids":["https://openalex.org/I4210158387"]},{"raw_affiliation_string":"National Laboratory of Biosciences, Campinas, Brazil","institution_ids":["https://openalex.org/I4210158387"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072224258","display_name":"Tiago J. P. Sobreira","orcid":"https://orcid.org/0000-0002-0217-0084"},"institutions":[{"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":"Tiago JP Sobreira","raw_affiliation_strings":["National Laboratory of Biosciences, P.O. Box 6192, CEP 13083-970, Campinas, SP, Brazil","National Laboratory of Biosciences, Campinas, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Laboratory of Biosciences, P.O. Box 6192, CEP 13083-970, Campinas, SP, Brazil","institution_ids":["https://openalex.org/I4210158387"]},{"raw_affiliation_string":"National Laboratory of Biosciences, Campinas, Brazil","institution_ids":["https://openalex.org/I4210158387"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109131039","display_name":"Paulo. S. Lopes-de Oliveira","orcid":null},"institutions":[{"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 SL de Oliveira","raw_affiliation_strings":["National Laboratory of Biosciences, P,O, Box 6192, CEP 13083-970 Campinas, SP, Brazil. paulo.oliveira@lnbio.cnpem.br","National Laboratory of Biosciences, Campinas, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Laboratory of Biosciences, P,O, Box 6192, CEP 13083-970 Campinas, SP, Brazil. paulo.oliveira@lnbio.cnpem.br","institution_ids":["https://openalex.org/I4210158387"]},{"raw_affiliation_string":"National Laboratory of Biosciences, Campinas, Brazil","institution_ids":["https://openalex.org/I4210158387"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":5.4084,"has_fulltext":true,"cited_by_count":116,"citation_normalized_percentile":{"value":0.9660811,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"15","issue":"1","first_page":"197","last_page":"197"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6489999890327454,"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":0.6489999890327454,"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":0.1462000012397766,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.025599999353289604,"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/plug-in","display_name":"Plug-in","score":0.8663461208343506},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.7082261443138123},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6084263920783997},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5118460059165955},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4919140338897705},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.38097238540649414},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29496490955352783},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24599874019622803},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21565255522727966},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10482892394065857}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.8663461208343506},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7082261443138123},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6084263920783997},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5118460059165955},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4919140338897705},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.38097238540649414},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29496490955352783},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24599874019622803},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21565255522727966},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10482892394065857},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":"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":"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","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}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-15-197","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-197","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-197","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:24938294","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24938294","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:europepmc.org:3043619","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4071799","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-197","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-197","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-197","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":[],"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/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2019498797.pdf","grobid_xml":"https://content.openalex.org/works/W2019498797.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1517566065","https://openalex.org/W1593939129","https://openalex.org/W1969370763","https://openalex.org/W1977444582","https://openalex.org/W1981064967","https://openalex.org/W2004175162","https://openalex.org/W2016936988","https://openalex.org/W2019951137","https://openalex.org/W2031194866","https://openalex.org/W2031337267","https://openalex.org/W2058463742","https://openalex.org/W2063725620","https://openalex.org/W2066143642","https://openalex.org/W2080653934","https://openalex.org/W2081702044","https://openalex.org/W2091563009","https://openalex.org/W2103794058","https://openalex.org/W2105902442","https://openalex.org/W2112109058","https://openalex.org/W2112794559","https://openalex.org/W2118382442","https://openalex.org/W2123440974","https://openalex.org/W2128402268","https://openalex.org/W2132395520","https://openalex.org/W2140407975","https://openalex.org/W2142757818","https://openalex.org/W2144258433","https://openalex.org/W2148219066","https://openalex.org/W2151345203","https://openalex.org/W2163352757","https://openalex.org/W2164088236","https://openalex.org/W2164741953","https://openalex.org/W2166225722","https://openalex.org/W2320259278","https://openalex.org/W4230982142"],"related_works":["https://openalex.org/W4287378204","https://openalex.org/W2981957539","https://openalex.org/W47352601","https://openalex.org/W2545422590","https://openalex.org/W4240705470","https://openalex.org/W2945311252","https://openalex.org/W631546281","https://openalex.org/W4213354039","https://openalex.org/W2266220644","https://openalex.org/W88292646"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"characterization":[2],"of":[3,20,24,34,94,103,112,123,129,138,154,169,176,184],"protein":[4,35,50],"binding":[5],"sites":[6],"is":[7,28,39,85,125,198,204,236],"a":[8,17,72,86,135,207,231],"major":[9],"challenge":[10],"in":[11,44,59,143],"computational":[12],"biology.":[13],"Proteins":[14],"interact":[15],"with":[16,108,152,230],"wide":[18],"variety":[19],"molecules":[21],"and":[22,66,75,81,149,222],"understanding":[23],"such":[25],"complex":[26],"interactions":[27],"essential":[29],"to":[30,41,56,145,191],"gain":[31],"deeper":[32],"knowledge":[33],"function.":[36],"Shape":[37],"complementarity":[38],"known":[40,140],"be":[42,57],"important":[43],"determining":[45],"protein-ligand":[46],"interactions.":[47],"Furthermore,":[48],"these":[49],"structural":[51],"features":[52],"have":[53],"been":[54],"shown":[55],"useful":[58],"assisting":[60],"medicinal":[61],"chemists":[62],"during":[63],"lead":[64],"discovery":[65],"optimization.":[67],"RESULTS:":[68],"We":[69],"developed":[70],"KVFinder,":[71],"highly":[73,223],"versatile":[74],"easy-to-use":[76],"tool":[77],"for":[78],"cavity":[79,104,117,225],"prospection":[80,128,178,226],"spatial":[82],"characterization.":[83],"KVFinder":[84,124,197,214,235],"geometry-based":[87],"method":[88],"that":[89],"has":[90],"an":[91],"innovative":[92],"customization":[93],"the":[95,101,109,120,126,155,160,170],"search":[96],"space.":[97],"This":[98],"feature":[99],"provides":[100],"possibility":[102],"segmentation,":[105],"which":[106],"alongside":[107,229],"large":[110],"set":[111],"customizable":[113,186,221],"parameters,":[114],"allows":[115],"detailed":[116,224],"analyses.":[118],"Although":[119],"main":[121],"focus":[122],"steered":[127],"cavities,":[130],"we":[131,164,188],"tested":[132],"it":[133,151,203],"against":[134],"benchmark":[136],"dataset":[137],"198":[139],"drug":[141],"targets":[142],"order":[144],"validate":[146],"our":[147],"software":[148],"compare":[150],"some":[153],"largely":[156],"accepted":[157],"methods.":[158,179,196],"Using":[159],"one":[161,183],"click":[162],"mode,":[163],"performed":[165],"better":[166],"than":[167],"most":[168],"other":[171,194],"methods,":[172],"staying":[173],"behind":[174],"only":[175],"hybrid":[177],"When":[180],"using":[181],"just":[182],"KVFinder's":[185],"features,":[187,218],"were":[189],"able":[190],"outperform":[192],"all":[193],"compared":[195],"also":[199],"user":[200],"friendly,":[201],"as":[202,206],"available":[205,238],"PyMOL":[208],"plugin,":[209],"or":[210],"command-line":[211],"version.":[212],"CONCLUSION:":[213],"presents":[215],"novel":[216],"usability":[217],"granting":[219],"full":[220],"on":[227,239],"proteins,":[228],"friendly":[232],"graphical":[233],"interface.":[234],"freely":[237],"http://lnbio.cnpem.br/bioinformatics/main/software/.":[240]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":15},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":7},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2016-06-24T00:00:00"}
