{"id":"https://openalex.org/W4385296227","doi":"https://doi.org/10.1021/acs.jcim.3c00745","title":"SurfPB: A GPU-Accelerated Electrostatic Calculation and Visualization Tool for Biomolecules","display_name":"SurfPB: A GPU-Accelerated Electrostatic Calculation and Visualization Tool for Biomolecules","publication_year":2023,"publication_date":"2023-07-27","ids":{"openalex":"https://openalex.org/W4385296227","doi":"https://doi.org/10.1021/acs.jcim.3c00745","pmid":"https://pubmed.ncbi.nlm.nih.gov/37500509"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00745","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00745","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/A5053569009","display_name":"Jun Liao","orcid":"https://orcid.org/0000-0002-2677-8465"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Liao","raw_affiliation_strings":["Biomolecular Physics and Modeling Group, School of Physics Huazhong University of Science and Technology, Wuhan 430074, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomolecular Physics and Modeling Group, School of Physics Huazhong University of Science and Technology, Wuhan 430074, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012574036","display_name":"Zirui Shu","orcid":null},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zirui Shu","raw_affiliation_strings":["Biomolecular Physics and Modeling Group, School of Physics Huazhong University of Science and Technology, Wuhan 430074, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomolecular Physics and Modeling Group, School of Physics Huazhong University of Science and Technology, Wuhan 430074, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020639373","display_name":"Junyong Gao","orcid":null},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junyong Gao","raw_affiliation_strings":["Biomolecular Physics and Modeling Group, School of Physics Huazhong University of Science and Technology, Wuhan 430074, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomolecular Physics and Modeling Group, School of Physics Huazhong University of Science and Technology, Wuhan 430074, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086615056","display_name":"Mincong Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mincong Wu","raw_affiliation_strings":["Biomolecular Physics and Modeling Group, School of Physics Huazhong University of Science and Technology, Wuhan 430074, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomolecular Physics and Modeling Group, School of Physics Huazhong University of Science and Technology, Wuhan 430074, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101848297","display_name":"Changjun Chen","orcid":"https://orcid.org/0000-0002-6188-5223"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Changjun Chen","raw_affiliation_strings":["Biomolecular Physics and Modeling Group, School of Physics Huazhong University of Science and Technology, Wuhan 430074, Hubei, China"],"raw_orcid":"https://orcid.org/0000-0002-6188-5223","affiliations":[{"raw_affiliation_string":"Biomolecular Physics and Modeling Group, School of Physics Huazhong University of Science and Technology, Wuhan 430074, Hubei, China","institution_ids":["https://openalex.org/I47720641"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5101848297"],"corresponding_institution_ids":["https://openalex.org/I47720641"],"apc_list":null,"apc_paid":null,"fwci":0.5382,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.68097689,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"63","issue":"15","first_page":"4490","last_page":"4496"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9988999962806702,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9760000109672546,"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/visualization","display_name":"Visualization","score":0.6688998937606812},{"id":"https://openalex.org/keywords/biomolecule","display_name":"Biomolecule","score":0.652834951877594},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5447214245796204},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.35981041193008423},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3271678686141968},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.20970919728279114},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.19118237495422363}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6688998937606812},{"id":"https://openalex.org/C49853544","wikidata":"https://www.wikidata.org/wiki/Q206229","display_name":"Biomolecule","level":2,"score":0.652834951877594},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5447214245796204},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.35981041193008423},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3271678686141968},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.20970919728279114},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.19118237495422363}],"mesh":[{"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":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c00745","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00745","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:37500509","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37500509","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}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8799999952316284,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G6155072622","display_name":null,"funder_award_id":"32271290","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1496452440","https://openalex.org/W1521376799","https://openalex.org/W1625910593","https://openalex.org/W1968707111","https://openalex.org/W1968984443","https://openalex.org/W1969910482","https://openalex.org/W1972452016","https://openalex.org/W1976499671","https://openalex.org/W1979683091","https://openalex.org/W1984157110","https://openalex.org/W1984951753","https://openalex.org/W1994662101","https://openalex.org/W2000588442","https://openalex.org/W2007258535","https://openalex.org/W2028031397","https://openalex.org/W2030609780","https://openalex.org/W2039833566","https://openalex.org/W2058004635","https://openalex.org/W2082363359","https://openalex.org/W2093381148","https://openalex.org/W2095719702","https://openalex.org/W2101936319","https://openalex.org/W2106140689","https://openalex.org/W2106956326","https://openalex.org/W2110720709","https://openalex.org/W2118233996","https://openalex.org/W2120795798","https://openalex.org/W2132262459","https://openalex.org/W2145803858","https://openalex.org/W2157281740","https://openalex.org/W2165327829","https://openalex.org/W2170802700","https://openalex.org/W2329540625","https://openalex.org/W2404280981","https://openalex.org/W2515356632","https://openalex.org/W2600950672","https://openalex.org/W2897759135","https://openalex.org/W2922133186","https://openalex.org/W2968876990","https://openalex.org/W2980169571","https://openalex.org/W3104537585","https://openalex.org/W3157133607","https://openalex.org/W3174415140","https://openalex.org/W3211407451","https://openalex.org/W4206206094","https://openalex.org/W4213188717","https://openalex.org/W4221040627","https://openalex.org/W4221095170","https://openalex.org/W4282006454","https://openalex.org/W4286382909","https://openalex.org/W4293003482"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2367089784","https://openalex.org/W4281383848","https://openalex.org/W2344707987","https://openalex.org/W3021795417","https://openalex.org/W3182059148","https://openalex.org/W2914491564","https://openalex.org/W4240108311","https://openalex.org/W145536452"],"abstract_inverted_index":{"In":[0,48],"this":[1],"work,":[2],"we":[3,76],"present":[4],"SurfPB":[5],"as":[6,73],"a":[7,56,78,97,111],"useful":[8],"tool":[9],"for":[10,82],"the":[11,22,38,40,44,50,89,93,107],"study":[12],"of":[13,37],"biomolecules.":[14],"It":[15,84],"can":[16,52],"do":[17],"many":[18],"typical":[19],"calculations,":[20,39],"including":[21],"molecular":[23,108],"surface,":[24],"electrostatic":[25,102],"potential,":[26],"solvation":[27],"free":[28,33],"energy,":[29],"entropy,":[30],"and":[31,61,91],"binding":[32],"energy.":[34],"Among":[35],"all":[36],"entropy":[41],"calculation":[42,51,95],"is":[43,69],"most":[45],"time-consuming":[46],"one.":[47],"SurfPB,":[49],"be":[53],"performed":[54],"in":[55,96,110],"vacuum":[57],"or":[58],"implicit":[59],"solvent":[60],"accelerated":[62,70],"on":[63,71,106],"GPU.":[64],"The":[65,100],"Poisson-Boltzmann":[66],"equation":[67],"solver":[68],"GPU":[72],"well.":[74],"Moreover,":[75],"developed":[77],"graphical":[79],"user":[80],"interface":[81],"SurfPB.":[83],"allows":[85],"users":[86],"to":[87],"input":[88],"parameters":[90],"complete":[92],"whole":[94],"visual":[98],"way.":[99],"calculated":[101],"potentials":[103],"are":[104],"shown":[105],"surface":[109],"three-dimensional":[112],"scene.":[113]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}