{"id":"https://openalex.org/W2154388132","doi":"https://doi.org/10.1093/bioinformatics/bti523","title":"PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes","display_name":"PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes","publication_year":2005,"publication_date":"2005-06-02","ids":{"openalex":"https://openalex.org/W2154388132","doi":"https://doi.org/10.1093/bioinformatics/bti523","mag":"2154388132","pmid":"https://pubmed.ncbi.nlm.nih.gov/15932902"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti523","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti523","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/15/3316/50340674/bioinformatics_21_15_3316.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/15/3316/50340674/bioinformatics_21_15_3316.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046318723","display_name":"Swanand Gore","orcid":"https://orcid.org/0000-0001-7468-6269"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Swanand P. Gore","raw_affiliation_strings":["Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK. swanand@cryst.bioc.cam.ac.uk","Department of Biochemistry, University of Cambridge  80 Tennis Court Road, Cambridge, CB2 1GA, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK. swanand@cryst.bioc.cam.ac.uk","institution_ids":["https://openalex.org/I241749"]},{"raw_affiliation_string":"Department of Biochemistry, University of Cambridge  80 Tennis Court Road, Cambridge, CB2 1GA, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078733447","display_name":"David F. Burke","orcid":"https://orcid.org/0000-0001-8830-3951"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David F. Burke","raw_affiliation_strings":["Department of Biochemistry, University of Cambridge  80 Tennis Court Road, Cambridge, CB2 1GA, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Cambridge  80 Tennis Court Road, Cambridge, CB2 1GA, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001029093","display_name":"Tom L. Blundell","orcid":"https://orcid.org/0000-0002-2708-8992"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Tom L. Blundell","raw_affiliation_strings":["Department of Biochemistry, University of Cambridge  80 Tennis Court Road, Cambridge, CB2 1GA, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Cambridge  80 Tennis Court Road, Cambridge, CB2 1GA, UK","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2641,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.78497133,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"21","issue":"15","first_page":"3316","last_page":"3317"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.32690000534057617,"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":0.32690000534057617,"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/T11162","display_name":"Enzyme Structure and Function","score":0.21649999916553497,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","score":0.12300000339746475,"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/voronoi-diagram","display_name":"Voronoi diagram","score":0.867077648639679},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.837462306022644},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7151920795440674},{"id":"https://openalex.org/keywords/centroidal-voronoi-tessellation","display_name":"Centroidal Voronoi tessellation","score":0.6155517101287842},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6149898767471313},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.5581969022750854},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.5347892642021179},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.532884955406189},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4381246864795685},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.41860198974609375},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.35057055950164795},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34196269512176514},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14506438374519348},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.10167643427848816}],"concepts":[{"id":"https://openalex.org/C24881265","wikidata":"https://www.wikidata.org/wiki/Q757267","display_name":"Voronoi diagram","level":2,"score":0.867077648639679},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.837462306022644},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7151920795440674},{"id":"https://openalex.org/C205672865","wikidata":"https://www.wikidata.org/wiki/Q5062961","display_name":"Centroidal Voronoi tessellation","level":3,"score":0.6155517101287842},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6149898767471313},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.5581969022750854},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.5347892642021179},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.532884955406189},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4381246864795685},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.41860198974609375},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35057055950164795},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34196269512176514},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14506438374519348},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.10167643427848816},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti523","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti523","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/15/3316/50340674/bioinformatics_21_15_3316.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15932902","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15932902","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti523","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti523","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/15/3316/50340674/bioinformatics_21_15_3316.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Sustainable cities and communities","id":"https://metadata.un.org/sdg/11","score":0.47999998927116394}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321847","display_name":"Cambridge Commonwealth Trust","ror":"https://ror.org/05sprqy15"},{"id":"https://openalex.org/F4320321848","display_name":"Cambridge Trust","ror":"https://ror.org/05sprqy15"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2154388132.pdf"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2015403140","https://openalex.org/W2081897966","https://openalex.org/W2123768693","https://openalex.org/W2130009286","https://openalex.org/W2140321728","https://openalex.org/W2153504150"],"related_works":["https://openalex.org/W2059217232","https://openalex.org/W1992160534","https://openalex.org/W2371724110","https://openalex.org/W1930867958","https://openalex.org/W1995318580","https://openalex.org/W2041214247","https://openalex.org/W2133344964","https://openalex.org/W4206423751","https://openalex.org/W2150727083","https://openalex.org/W2051752778"],"abstract_inverted_index":{"SUMMARY:":[0],"Voronoi":[1,29,62],"tessellation":[2,63,113],"has":[3],"proved":[4],"to":[5,110],"be":[6,120],"a":[7,18,38,53,65,70,74,103,108,127],"useful":[8],"tool":[9,60],"in":[10,69,94],"protein":[11,34,67],"structure":[12],"analysis.":[13],"We":[14],"have":[15],"developed":[16],"PROVAT,":[17],"versatile":[19],"public":[20],"domain":[21],"software":[22,48],"that":[23,43,106],"enables":[24],"computation":[25],"and":[26,33,78,134],"visualization":[27,101],"of":[28,31,40,58,64],"tessellations":[30],"proteins":[32],"complexes.":[35],"It":[36],"is":[37,97],"set":[39],"Python":[41,90],"scripts":[42],"integrate":[44],"freely":[45],"available":[46],"specialized":[47],"(Qhull,":[49],"Pymol":[50,104],"etc.)":[51],"into":[52],"pipeline.":[54],"The":[55,89],"calculation":[56,131],"component":[57],"the":[59,95,100,112],"computes":[61],"given":[66],"system":[68],"way":[71],"described":[72],"by":[73,99],"user-supplied":[75],"XML":[76],"recipe":[77],"stores":[79],"resulting":[80],"neighbourhood":[81],"information":[82],"as":[83],"text":[84],"files":[85],"with":[86],"various":[87],"styles.":[88],"pickle":[91],"file":[92],"generated":[93],"process":[96],"used":[98],"component,":[102,132],"plug-in,":[105],"offers":[107],"GUI":[109],"explore":[111],"visually.":[114],"AVAILABILITY:":[115],"PROVAT":[116],"source":[117],"code":[118],"can":[119],"downloaded":[121],"from":[122],"http://raven.bioc.cam.ac.uk/~swanand/Provat1,":[123],"which":[124],"also":[125],"provides":[126],"webserver":[128],"for":[129],"its":[130],"documentation":[133],"examples.":[135]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}