{"id":"https://openalex.org/W4400325322","doi":"https://doi.org/10.1021/acs.jcim.4c00641","title":"Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models","display_name":"Accurately Computing the Interacted Volume of Molecules over Their 3D Mesh Models","publication_year":2024,"publication_date":"2024-07-04","ids":{"openalex":"https://openalex.org/W4400325322","doi":"https://doi.org/10.1021/acs.jcim.4c00641","pmid":"https://pubmed.ncbi.nlm.nih.gov/38962905"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c00641","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00641","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/A5114187359","display_name":"Fangting Li","orcid":null},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fangting Li","raw_affiliation_strings":["College of Electrical Engineering, Sichuan University, Chengdu, Sichuan 610065, China"],"raw_orcid":"https://orcid.org/0009-0000-5926-4199","affiliations":[{"raw_affiliation_string":"College of Electrical Engineering, Sichuan University, Chengdu, Sichuan 610065, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101925716","display_name":"Kun Lv","orcid":"https://orcid.org/0000-0002-0354-0235"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kun Lv","raw_affiliation_strings":["College of Electrical Engineering, Sichuan University, Chengdu, Sichuan 610065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Electrical Engineering, Sichuan University, Chengdu, Sichuan 610065, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100370781","display_name":"Xiaohua Liu","orcid":"https://orcid.org/0000-0001-9555-0555"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohua Liu","raw_affiliation_strings":["Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China"],"raw_orcid":"https://orcid.org/0000-0001-9555-0555","affiliations":[{"raw_affiliation_string":"Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000050521","display_name":"Yuqiao Zhou","orcid":"https://orcid.org/0000-0003-3490-4182"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yuqiao Zhou","raw_affiliation_strings":["Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100399921","display_name":"Kai Liu","orcid":"https://orcid.org/0000-0002-6433-6529"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kai Liu","raw_affiliation_strings":["College of Electrical Engineering, Sichuan University, Chengdu, Sichuan 610065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Electrical Engineering, Sichuan University, Chengdu, Sichuan 610065, China","institution_ids":["https://openalex.org/I24185976"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5000050521","https://openalex.org/A5100399921"],"corresponding_institution_ids":["https://openalex.org/I24185976"],"apc_list":null,"apc_paid":null,"fwci":0.6081,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.61414899,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"64","issue":"14","first_page":"5535","last_page":"5546"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10405","display_name":"Advanced Polymer Synthesis and Characterization","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10405","display_name":"Advanced Polymer Synthesis and Characterization","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9926999807357788,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/volume","display_name":"Volume (thermodynamics)","score":0.6527992486953735},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40849679708480835},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3708842694759369},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.18757250905036926},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.11678886413574219}],"concepts":[{"id":"https://openalex.org/C20556612","wikidata":"https://www.wikidata.org/wiki/Q4469374","display_name":"Volume (thermodynamics)","level":2,"score":0.6527992486953735},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40849679708480835},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3708842694759369},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.18757250905036926},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.11678886413574219}],"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":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","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":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","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.4c00641","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00641","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:38962905","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38962905","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":[],"awards":[{"id":"https://openalex.org/G4890951106","display_name":null,"funder_award_id":"22188101","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":42,"referenced_works":["https://openalex.org/W576840513","https://openalex.org/W1874694348","https://openalex.org/W1993526279","https://openalex.org/W1995222467","https://openalex.org/W2009398710","https://openalex.org/W2021968989","https://openalex.org/W2025824904","https://openalex.org/W2090755068","https://openalex.org/W2091439890","https://openalex.org/W2093057811","https://openalex.org/W2105533397","https://openalex.org/W2132525235","https://openalex.org/W2467400748","https://openalex.org/W2639728117","https://openalex.org/W2734490269","https://openalex.org/W2735655854","https://openalex.org/W2885492408","https://openalex.org/W2952782546","https://openalex.org/W2971791401","https://openalex.org/W2980706490","https://openalex.org/W3005308876","https://openalex.org/W3006662681","https://openalex.org/W3011847032","https://openalex.org/W3124681459","https://openalex.org/W3130792276","https://openalex.org/W3135780247","https://openalex.org/W3152766923","https://openalex.org/W3154825709","https://openalex.org/W3195475363","https://openalex.org/W4233857083","https://openalex.org/W4233998925","https://openalex.org/W4296959088","https://openalex.org/W4318215238","https://openalex.org/W4366163487","https://openalex.org/W4377825750","https://openalex.org/W4379616753","https://openalex.org/W4380990632","https://openalex.org/W4386288220","https://openalex.org/W4387426283","https://openalex.org/W4388162958","https://openalex.org/W4388462156","https://openalex.org/W4388573553"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"For":[0],"quickly":[1],"predicting":[2],"the":[3,17,29,45,48,76,82,91,96,172,186,191],"rational":[4],"arrangement":[5],"of":[6,20,47,81,86,118,134,169],"catalysts":[7],"and":[8,138,193],"substrates,":[9],"we":[10,54,74,107,123],"previously":[11],"proposed":[12],"a":[13,56,69,125],"method":[14,58,155],"to":[15,38],"calculate":[16],"interacted":[18,64,119,197],"volumes":[19],"molecules":[21,88],"over":[22],"their":[23],"3D":[24,77],"point":[25,34],"cloud":[26],"models.":[27],"However,":[28],"nonuniform":[30],"density":[31],"in":[32,41,99,132,159,195],"molecular":[33,63],"clouds":[35],"may":[36],"lead":[37],"incomplete":[39],"contours":[40],"some":[42],"slices,":[43],"reducing":[44],"accuracy":[46,158,192],"previous":[49,187],"method.":[50],"In":[51,121],"this":[52],"paper,":[53],"propose":[55],"two-step":[57],"for":[59,128,139],"more":[60],"accurately":[61,108],"computing":[62,129],"volumes.":[65,120,198],"First,":[66],"by":[67,103,143],"employing":[68],"prematched":[70],"mesh":[71,79],"slicing":[72],"method,":[73],"layer":[75],"triangular":[78],"models":[80],"electrostatic":[83],"potential":[84],"isosurfaces":[85],"two":[87],"globally,":[89],"transforming":[90],"volume":[92],"calculation":[93,117],"into":[94],"finding":[95],"intersecting":[97,110,130],"areas":[98,131],"each":[100,113],"layer.":[101],"Next,":[102],"subdividing":[104],"polygonal":[105],"edges,":[106],"identify":[109],"parts":[111],"within":[112],"layer,":[114],"ensuring":[115],"precise":[116],"addition,":[122],"present":[124],"concise":[126],"overview":[127],"cases":[133],"multiple":[135],"contour":[136],"intersections":[137],"improving":[140,190],"computational":[141],"efficiency":[142],"incorporating":[144],"bounding":[145],"boxes":[146],"at":[147],"three":[148],"stages.":[149],"Experimental":[150],"results":[151],"demonstrate":[152],"that":[153],"our":[154,176],"maintains":[156],"high":[157],"different":[160],"experimental":[161,174],"data":[162],"sets,":[163],"with":[164],"an":[165],"average":[166,177],"relative":[167,178],"error":[168,179],"0.16%.":[170],"On":[171],"same":[173],"setup,":[175],"is":[180,183],"0.07%,":[181],"which":[182],"lower":[184],"than":[185],"algorithm's":[188],"1.73%,":[189],"stability":[194],"calculating":[196]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
