{"id":"https://openalex.org/W3216247503","doi":"https://doi.org/10.1109/jbhi.2021.3130897","title":"Particle-Based Calculation and Visualization of Protein Cavities Using SES Models","display_name":"Particle-Based Calculation and Visualization of Protein Cavities Using SES Models","publication_year":2021,"publication_date":"2021-11-29","ids":{"openalex":"https://openalex.org/W3216247503","doi":"https://doi.org/10.1109/jbhi.2021.3130897","mag":"3216247503","pmid":"https://pubmed.ncbi.nlm.nih.gov/34843433"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2021.3130897","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2021.3130897","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","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":null,"display_name":"Li Feng","orcid":null},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Feng","raw_affiliation_strings":["Yanshan University, Hebei, Qinhuangdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yanshan University, Hebei, Qinhuangdao, China","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Feng Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Wang","raw_affiliation_strings":["Yanshan University, Hebei, Qinhuangdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yanshan University, Hebei, Qinhuangdao, China","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jian Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Zhang","raw_affiliation_strings":["Yanshan University, Hebei, Qinhuangdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yanshan University, Hebei, Qinhuangdao, China","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yong Tang","orcid":null},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yong Tang","raw_affiliation_strings":["Yanshan University, Hebei, Qinhuangdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yanshan University, Hebei, Qinhuangdao, China","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jing Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Zhao","raw_affiliation_strings":["Yanshan University, Hebei, Qinhuangdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yanshan University, Hebei, Qinhuangdao, China","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Lisha Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lisha Zhou","raw_affiliation_strings":["Yanshan University, Hebei, Qinhuangdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yanshan University, Hebei, Qinhuangdao, China","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jiayan Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiayan Wang","raw_affiliation_strings":["Yanshan University, Hebei, Qinhuangdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yanshan University, Hebei, Qinhuangdao, China","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Dongliang Guo","orcid":"https://orcid.org/0000-0001-9935-7373"},"institutions":[{"id":"https://openalex.org/I39333907","display_name":"Yanshan University","ror":"https://ror.org/02txfnf15","country_code":"CN","type":"education","lineage":["https://openalex.org/I39333907"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongliang Guo","raw_affiliation_strings":["Yanshan University and Computer Virtualization Technology and System Integration Laboratory, Hebei, Qinhuangdao, China"],"raw_orcid":"https://orcid.org/0000-0001-9935-7373","affiliations":[{"raw_affiliation_string":"Yanshan University and Computer Virtualization Technology and System Integration Laboratory, Hebei, Qinhuangdao, China","institution_ids":["https://openalex.org/I39333907"]}]},{"author_position":"last","author":{"id":null,"display_name":"Amit Kumar Singh","orcid":"https://orcid.org/0000-0001-7359-2068"},"institutions":[{"id":"https://openalex.org/I11793825","display_name":"National Institute of Technology Patna","ror":"https://ror.org/056wyhh33","country_code":"IN","type":"education","lineage":["https://openalex.org/I11793825","https://openalex.org/I4210152752"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Amit Kumar Singh","raw_affiliation_strings":["IEEE Department of Computer Science &amp; Engineering, National Institute of Technology Patna, Bihar, India"],"raw_orcid":"https://orcid.org/0000-0001-7359-2068","affiliations":[{"raw_affiliation_string":"IEEE Department of Computer Science &amp; Engineering, National Institute of Technology Patna, Bihar, India","institution_ids":["https://openalex.org/I11793825"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1586,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.49074896,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":"26","issue":"6","first_page":"2447","last_page":"2457"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.15000000596046448,"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":0.15000000596046448,"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":0.08340000361204147,"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/T13052","display_name":"Molecular Communication and Nanonetworks","score":0.06970000267028809,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7649999856948853},{"id":"https://openalex.org/keywords/position","display_name":"Position (finance)","score":0.6186000108718872},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5080000162124634},{"id":"https://openalex.org/keywords/interactive-visualization","display_name":"Interactive visualization","score":0.44290000200271606},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.40459999442100525},{"id":"https://openalex.org/keywords/perception","display_name":"Perception","score":0.3158000111579895},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.31060001254081726}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7649999856948853},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.723800003528595},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.6186000108718872},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5080000162124634},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.44290000200271606},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.43149998784065247},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.40459999442100525},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3474999964237213},{"id":"https://openalex.org/C26760741","wikidata":"https://www.wikidata.org/wiki/Q160402","display_name":"Perception","level":2,"score":0.3158000111579895},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.313400000333786},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.31060001254081726},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3066999912261963},{"id":"https://openalex.org/C2989223519","wikidata":"https://www.wikidata.org/wiki/Q349669","display_name":"Resonant cavity","level":3,"score":0.3043000102043152},{"id":"https://openalex.org/C89992363","wikidata":"https://www.wikidata.org/wiki/Q5961558","display_name":"Track (disk drive)","level":2,"score":0.29820001125335693},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.2802000045776367},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.2745000123977661},{"id":"https://openalex.org/C18762648","wikidata":"https://www.wikidata.org/wiki/Q42213","display_name":"Work (physics)","level":2,"score":0.26579999923706055},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2639999985694885},{"id":"https://openalex.org/C77660652","wikidata":"https://www.wikidata.org/wiki/Q150971","display_name":"Computer graphics","level":2,"score":0.26269999146461487},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.2599000036716461},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2597000002861023},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2563000023365021}],"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":"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2021.3130897","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2021.3130897","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:34843433","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34843433","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5447342375","display_name":null,"funder_award_id":"61802334","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7104478822","display_name":null,"funder_award_id":"61902340","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1517566065","https://openalex.org/W1911053776","https://openalex.org/W2005433675","https://openalex.org/W2014394152","https://openalex.org/W2019498797","https://openalex.org/W2019951137","https://openalex.org/W2034542871","https://openalex.org/W2045670663","https://openalex.org/W2058463742","https://openalex.org/W2067691029","https://openalex.org/W2082917051","https://openalex.org/W2091563009","https://openalex.org/W2105902442","https://openalex.org/W2112109058","https://openalex.org/W2112961542","https://openalex.org/W2115513040","https://openalex.org/W2116703791","https://openalex.org/W2131777290","https://openalex.org/W2140387095","https://openalex.org/W2162785950","https://openalex.org/W2164088236","https://openalex.org/W2166225722","https://openalex.org/W2169242540","https://openalex.org/W2467187082","https://openalex.org/W2467480556","https://openalex.org/W2488878161","https://openalex.org/W2770354547","https://openalex.org/W2909813131","https://openalex.org/W3030441522","https://openalex.org/W3096764687","https://openalex.org/W6637799307","https://openalex.org/W6711911964","https://openalex.org/W6736683735"],"related_works":[],"abstract_inverted_index":{"The":[0,39],"analysis":[1],"of":[2,26,30,70,86],"molecular":[3],"cavities,":[4],"where":[5],"ligands":[6],"interact":[7],"with":[8,136],"protein":[9,16,89],"structures,":[10],"plays":[11],"a":[12,23,63,87,103],"critical":[13],"role":[14],"in":[15,34,55],"structure-based":[17],"drug":[18],"design.":[19],"However,":[20],"it":[21],"is":[22],"challenge":[24],"because":[25],"the":[27,31,67,76,80,92,100,120,131,137],"ambiguous":[28],"definition":[29],"cavity":[32,36,71,96,121],"boundaries":[33,93],"most":[35],"detection":[37],"methods.":[38],"cavities":[40,54,112,133],"are":[41,48,134],"mostly":[42],"calculated":[43],"by":[44,113],"input":[45],"parameters,":[46],"which":[47],"difficult":[49],"for":[50,66],"users":[51,109],"to":[52,90,107,110,118],"visualize":[53],"interactive":[56,68,105],"ways.":[57],"In":[58],"this":[59],"paper,":[60],"we":[61],"propose":[62],"novel":[64],"method":[65,78,106],"exploration":[69],"calculation":[72],"and":[73,94,117,123,150],"visualization.":[74],"Firstly,":[75],"proposed":[77],"combines":[79],"two":[81],"solvent-excluded":[82],"surfaces":[83],"(SES)":[84],"models":[85],"given":[88],"define":[91],"provides":[95,102],"emission":[97],"points.":[98],"Secondly,":[99],"system":[101],"user-guided":[104],"allow":[108],"select":[111],"simply":[114],"clicking":[115],"operations":[116],"track":[119],"identify":[122,149],"filling":[124],"process":[125],"based":[126],"on":[127],"position":[128],"constraints.":[129],"Finally,":[130],"selected":[132],"represented":[135],"colorful":[138],"depth":[139],"perception":[140],"method.":[141],"Experiments":[142],"show":[143],"that":[144],"our":[145],"work":[146],"can":[147],"effectively":[148],"calculate":[151],"cavities.":[152]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2021-12-06T00:00:00"}
