{"id":"https://openalex.org/W2909813131","doi":"https://doi.org/10.1021/acs.jcim.8b00572","title":"CavVis\u2014A Field-of-View Geometric Algorithm for Protein Cavity Detection","display_name":"CavVis\u2014A Field-of-View Geometric Algorithm for Protein Cavity Detection","publication_year":2019,"publication_date":"2019-01-10","ids":{"openalex":"https://openalex.org/W2909813131","doi":"https://doi.org/10.1021/acs.jcim.8b00572","mag":"2909813131","pmid":"https://pubmed.ncbi.nlm.nih.gov/30629446"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.8b00572","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00572","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003620691","display_name":"Tiago M. C. Sim\u00f5es","orcid":"https://orcid.org/0000-0001-8858-0027"},"institutions":[{"id":"https://openalex.org/I161321875","display_name":"University of Beira Interior","ror":"https://ror.org/03nf36p02","country_code":"PT","type":"education","lineage":["https://openalex.org/I161321875"]},{"id":"https://openalex.org/I4210120471","display_name":"Instituto de Telecomunica\u00e7\u00f5es","ror":"https://ror.org/02ht4fk33","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210120471"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Tiago M. C. Sim\u00f5es","raw_affiliation_strings":["Departamento de Inform\u00e1tica, Universidade da Beira Interior, 6200-001 Covilh\u00e3, Portugal","Instituto de Telecomunica\u00e7\u00f5es, Delega\u00e7\u00e3o da Covilh\u00e3, 6200-001 Covilh\u00e3, Portugal"],"affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Universidade da Beira Interior, 6200-001 Covilh\u00e3, Portugal","institution_ids":["https://openalex.org/I161321875"]},{"raw_affiliation_string":"Instituto de Telecomunica\u00e7\u00f5es, Delega\u00e7\u00e3o da Covilh\u00e3, 6200-001 Covilh\u00e3, Portugal","institution_ids":["https://openalex.org/I4210120471"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053666594","display_name":"Abel Gomes","orcid":"https://orcid.org/0000-0002-5804-5717"},"institutions":[{"id":"https://openalex.org/I161321875","display_name":"University of Beira Interior","ror":"https://ror.org/03nf36p02","country_code":"PT","type":"education","lineage":["https://openalex.org/I161321875"]},{"id":"https://openalex.org/I4210120471","display_name":"Instituto de Telecomunica\u00e7\u00f5es","ror":"https://ror.org/02ht4fk33","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I4210120471"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Abel J. P. Gomes","raw_affiliation_strings":["Departamento de Inform\u00e1tica, Universidade da Beira Interior, 6200-001 Covilh\u00e3, Portugal","Instituto de Telecomunica\u00e7\u00f5es, Delega\u00e7\u00e3o da Covilh\u00e3, 6200-001 Covilh\u00e3, Portugal"],"affiliations":[{"raw_affiliation_string":"Departamento de Inform\u00e1tica, Universidade da Beira Interior, 6200-001 Covilh\u00e3, Portugal","institution_ids":["https://openalex.org/I161321875"]},{"raw_affiliation_string":"Instituto de Telecomunica\u00e7\u00f5es, Delega\u00e7\u00e3o da Covilh\u00e3, 6200-001 Covilh\u00e3, Portugal","institution_ids":["https://openalex.org/I4210120471"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5053666594"],"corresponding_institution_ids":["https://openalex.org/I161321875","https://openalex.org/I4210120471"],"apc_list":null,"apc_paid":null,"fwci":1.2882,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.79528081,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"59","issue":"2","first_page":"786","last_page":"796"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9828000068664551,"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":0.9828000068664551,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.979200005531311,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9767000079154968,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/ray-casting","display_name":"Ray casting","score":0.7505459785461426},{"id":"https://openalex.org/keywords/voxel","display_name":"Voxel","score":0.6602542996406555},{"id":"https://openalex.org/keywords/gaussian-surface","display_name":"Gaussian surface","score":0.6509183645248413},{"id":"https://openalex.org/keywords/molecular-graphics","display_name":"Molecular graphics","score":0.6492694020271301},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6108282804489136},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.5712121725082397},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics","score":0.5102148056030273},{"id":"https://openalex.org/keywords/visibility","display_name":"Visibility","score":0.5052464604377747},{"id":"https://openalex.org/keywords/surface","display_name":"Surface (topology)","score":0.4778306484222412},{"id":"https://openalex.org/keywords/point","display_name":"Point (geometry)","score":0.45862525701522827},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.45749908685684204},{"id":"https://openalex.org/keywords/gaussian","display_name":"Gaussian","score":0.43644025921821594},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.43390464782714844},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.41073620319366455},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.39429616928100586},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3566928505897522},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.3016209602355957},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.23256248235702515},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19853782653808594},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.17388644814491272},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.12316495180130005},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.10910743474960327},{"id":"https://openalex.org/keywords/volume-rendering","display_name":"Volume rendering","score":0.08840033411979675}],"concepts":[{"id":"https://openalex.org/C116108083","wikidata":"https://www.wikidata.org/wiki/Q1940131","display_name":"Ray casting","level":4,"score":0.7505459785461426},{"id":"https://openalex.org/C54170458","wikidata":"https://www.wikidata.org/wiki/Q663554","display_name":"Voxel","level":2,"score":0.6602542996406555},{"id":"https://openalex.org/C68806387","wikidata":"https://www.wikidata.org/wiki/Q2724617","display_name":"Gaussian surface","level":3,"score":0.6509183645248413},{"id":"https://openalex.org/C126766683","wikidata":"https://www.wikidata.org/wiki/Q6896006","display_name":"Molecular graphics","level":3,"score":0.6492694020271301},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6108282804489136},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.5712121725082397},{"id":"https://openalex.org/C77660652","wikidata":"https://www.wikidata.org/wiki/Q150971","display_name":"Computer graphics","level":2,"score":0.5102148056030273},{"id":"https://openalex.org/C123403432","wikidata":"https://www.wikidata.org/wiki/Q654068","display_name":"Visibility","level":2,"score":0.5052464604377747},{"id":"https://openalex.org/C2776799497","wikidata":"https://www.wikidata.org/wiki/Q484298","display_name":"Surface (topology)","level":2,"score":0.4778306484222412},{"id":"https://openalex.org/C28719098","wikidata":"https://www.wikidata.org/wiki/Q44946","display_name":"Point (geometry)","level":2,"score":0.45862525701522827},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.45749908685684204},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.43644025921821594},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.43390464782714844},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.41073620319366455},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.39429616928100586},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3566928505897522},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.3016209602355957},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.23256248235702515},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19853782653808594},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.17388644814491272},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12316495180130005},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.10910743474960327},{"id":"https://openalex.org/C30769735","wikidata":"https://www.wikidata.org/wiki/Q2165951","display_name":"Volume rendering","level":3,"score":0.08840033411979675},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C60799052","wikidata":"https://www.wikidata.org/wiki/Q46221","display_name":"Electric field","level":2,"score":0.0},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","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":"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":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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.8b00572","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00572","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:30629446","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30629446","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:ubibliorum.ubi.pt:10400.6/8295","is_oa":false,"landing_page_url":"http://hdl.handle.net/10400.6/8295","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4017497872","display_name":null,"funder_award_id":"UID/EEA/50008/2013","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G611427585","display_name":null,"funder_award_id":"SFRH/BD/99813/2014","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W950047984","https://openalex.org/W1490482062","https://openalex.org/W1505728031","https://openalex.org/W1517566065","https://openalex.org/W1984563996","https://openalex.org/W2019498797","https://openalex.org/W2019951137","https://openalex.org/W2027491603","https://openalex.org/W2029667189","https://openalex.org/W2031194866","https://openalex.org/W2051182208","https://openalex.org/W2054668663","https://openalex.org/W2058326046","https://openalex.org/W2058463742","https://openalex.org/W2059536443","https://openalex.org/W2063831812","https://openalex.org/W2063908367","https://openalex.org/W2067455153","https://openalex.org/W2076127975","https://openalex.org/W2087179087","https://openalex.org/W2095822427","https://openalex.org/W2112777640","https://openalex.org/W2112794559","https://openalex.org/W2116703791","https://openalex.org/W2123440974","https://openalex.org/W2130249022","https://openalex.org/W2132395520","https://openalex.org/W2132629607","https://openalex.org/W2140407975","https://openalex.org/W2141742950","https://openalex.org/W2146968309","https://openalex.org/W2164088236","https://openalex.org/W2166225722","https://openalex.org/W2169434145","https://openalex.org/W2244686166","https://openalex.org/W2266013672","https://openalex.org/W2312729996","https://openalex.org/W2467187082","https://openalex.org/W2488878161","https://openalex.org/W2549327495","https://openalex.org/W2621171687","https://openalex.org/W2770354547","https://openalex.org/W4230466483","https://openalex.org/W4233857083","https://openalex.org/W4250589301"],"related_works":["https://openalex.org/W1542109480","https://openalex.org/W2294494167","https://openalex.org/W2352781897","https://openalex.org/W2038255918","https://openalex.org/W2037810710","https://openalex.org/W1974904668","https://openalex.org/W2025457265","https://openalex.org/W2082728368","https://openalex.org/W2073105412","https://openalex.org/W2909813131"],"abstract_inverted_index":{"Several":[0],"geometric-based":[1],"methods":[2],"have":[3],"been":[4],"developed":[5],"for":[6],"the":[7,60,78,89],"last":[8],"two":[9],"to":[10,13,26,73],"three":[11,82],"decades":[12],"detect":[14],"and":[15,30,51,98],"identify":[16],"cavities":[17],"(i.e.,":[18,46],"putative":[19],"binding":[20],"sites)":[21],"on":[22,70],"proteins,":[23],"as":[24],"needed":[25],"study":[27],"protein-ligand":[28],"interactions":[29],"protein":[31,38,71],"docking.":[32],"This":[33,63],"paper":[34],"introduces":[35],"a":[36,47],"new":[37],"cavity":[39],"method,":[40],"called":[41],"CavVis,":[42],"which":[43],"combines":[44,81],"voxelization":[45],"grid":[48],"of":[49,55,68,91],"voxels)":[50],"an":[52],"analytic":[53],"formulation":[54],"Gaussian":[56],"surfaces":[57],"that":[58],"approximates":[59],"solvent-excluded":[61],"surface.":[62],"method":[64],"builds":[65],"upon":[66],"visibility":[67,79],"points":[69],"surface":[72,93],"find":[74],"its":[75],"cavities.":[76],"Specifically,":[77],"criterion":[80],"concepts":[83],"we":[84],"borrow":[85],"from":[86],"computer":[87],"graphics,":[88],"field-of-view":[90],"each":[92],"point,":[94],"voxel":[95],"ray":[96],"casting,":[97],"back-face":[99],"culling.":[100]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":7},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":2}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
