{"id":"https://openalex.org/W3195949190","doi":"https://doi.org/10.1093/bioinformatics/btab616","title":"Precise estimation of residue relative solvent accessible area from C\u03b1 atom distance matrix using a deep learning method","display_name":"Precise estimation of residue relative solvent accessible area from C\u03b1 atom distance matrix using a deep learning method","publication_year":2021,"publication_date":"2021-08-27","ids":{"openalex":"https://openalex.org/W3195949190","doi":"https://doi.org/10.1093/bioinformatics/btab616","mag":"3195949190","pmid":"https://pubmed.ncbi.nlm.nih.gov/34450651"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab616","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab616","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/1/94/49006269/btab616.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/1/94/49006269/btab616.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011520778","display_name":"Jianzhao Gao","orcid":"https://orcid.org/0000-0002-9943-4786"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianzhao Gao","raw_affiliation_strings":["School of Mathematical Sciences and LPMC, Nankai University , Tianjin 300071, China"],"raw_orcid":"https://orcid.org/0000-0002-9943-4786","affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences and LPMC, Nankai University , Tianjin 300071, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075817762","display_name":"Shuangjia Zheng","orcid":"https://orcid.org/0000-0001-9747-4285"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuangjia Zheng","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-Sen University , Guangzhou 510006, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-Sen University , Guangzhou 510006, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013953070","display_name":"Mengting Yao","orcid":"https://orcid.org/0000-0002-2163-3996"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengting Yao","raw_affiliation_strings":["School of Mathematical Sciences and LPMC, Nankai University , Tianjin 300071, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences and LPMC, Nankai University , Tianjin 300071, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010803769","display_name":"Peikun Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peikun Wu","raw_affiliation_strings":["School of Mathematical Sciences and LPMC, Nankai University , Tianjin 300071, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences and LPMC, Nankai University , Tianjin 300071, China","institution_ids":["https://openalex.org/I205237279"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5011520778"],"corresponding_institution_ids":["https://openalex.org/I205237279"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3965,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.58393785,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"38","issue":"1","first_page":"94","last_page":"98"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.847599983215332,"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":0.847599983215332,"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":0.059300001710653305,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.02759999968111515,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.6835218071937561},{"id":"https://openalex.org/keywords/solvent","display_name":"Solvent","score":0.5638930201530457},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.5005512237548828},{"id":"https://openalex.org/keywords/distance-matrices-in-phylogeny","display_name":"Distance matrices in phylogeny","score":0.4939466118812561},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45503824949264526},{"id":"https://openalex.org/keywords/atom","display_name":"Atom (system on chip)","score":0.430753618478775},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3803979158401489},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3396579623222351},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.33169010281562805},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.31925028562545776},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.22287800908088684},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.18621861934661865},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.12647384405136108}],"concepts":[{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.6835218071937561},{"id":"https://openalex.org/C2780471494","wikidata":"https://www.wikidata.org/wiki/Q146505","display_name":"Solvent","level":2,"score":0.5638930201530457},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.5005512237548828},{"id":"https://openalex.org/C5349765","wikidata":"https://www.wikidata.org/wiki/Q5282866","display_name":"Distance matrices in phylogeny","level":2,"score":0.4939466118812561},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45503824949264526},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.430753618478775},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3803979158401489},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3396579623222351},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.33169010281562805},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.31925028562545776},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.22287800908088684},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.18621861934661865},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.12647384405136108},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":null,"qualifier_name":null,"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":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab616","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab616","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/1/94/49006269/btab616.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34450651","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34450651","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/btab616","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab616","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/1/94/49006269/btab616.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2598587236","display_name":null,"funder_award_id":"11701296","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6626711343","display_name":null,"funder_award_id":"18JCQNJC09600","funder_id":"https://openalex.org/F4320323993","funder_display_name":"Natural Science Foundation of Tianjin City"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320323993","display_name":"Natural Science Foundation of Tianjin City","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1967058595","https://openalex.org/W1988075691","https://openalex.org/W2008708467","https://openalex.org/W2021217817","https://openalex.org/W2050270988","https://openalex.org/W2050625197","https://openalex.org/W2059067075","https://openalex.org/W2069163783","https://openalex.org/W2070778264","https://openalex.org/W2085277871","https://openalex.org/W2100908214","https://openalex.org/W2154106236","https://openalex.org/W2326199080","https://openalex.org/W2507606055","https://openalex.org/W2540069603","https://openalex.org/W2603587832","https://openalex.org/W2794226826","https://openalex.org/W2919756742","https://openalex.org/W2953873015","https://openalex.org/W2991877021","https://openalex.org/W3011946302","https://openalex.org/W3033505940","https://openalex.org/W4293003482","https://openalex.org/W6668313351"],"related_works":["https://openalex.org/W2032398765","https://openalex.org/W2391870038","https://openalex.org/W2053842772","https://openalex.org/W2053541600","https://openalex.org/W2354603059","https://openalex.org/W2602858595","https://openalex.org/W2151479006","https://openalex.org/W2073958536","https://openalex.org/W2084087543","https://openalex.org/W1517651240"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,78,156],"solvent":[2,20,131],"accessible":[3,21,132],"surface":[4,38],"is":[5,24,52,158],"an":[6],"essential":[7],"structural":[8],"property":[9],"measure":[10,27],"related":[11],"to":[12,28,128,146],"the":[13,30,36,49,67,73,118,125,130,147],"protein":[14,17,37,148,151],"structure":[15,149],"and":[16,115,150],"function.":[18],"Relative":[19],"area":[22,133],"(RSA)":[23],"a":[25,60,138],"standard":[26],"describe":[29],"degree":[31],"of":[32,41,86,120],"residue":[33],"exposure":[34,114],"in":[35],"or":[39],"inside":[40],"protein.":[42],"However,":[43],"this":[44,56],"computation":[45],"will":[46],"fail":[47],"when":[48],"residues":[50],"information":[51,136],"missing.":[53],"RESULTS:":[54],"In":[55],"article,":[57],"we":[58],"proposed":[59],"novel":[61],"method":[62,76,127,157],"for":[63],"estimation":[64],"RSA":[65,106],"using":[66,134],"C\u03b1":[68],"atom":[69],"distance":[70],"matrix":[71],"with":[72,137],"deep":[74,139],"learning":[75,140],"(EAGERER).":[77],"new":[79],"method,":[80],"EAGERER,":[81],"achieves":[82],"Pearson":[83,101],"correlation":[84,102],"coefficients":[85,103],"0.921-0.928":[87],"on":[88],"two":[89],"independent":[90],"test":[91],"datasets.":[92],"We":[93],"empirically":[94],"demonstrate":[95],"that":[96],"EAGERER":[97,123],"can":[98],"yield":[99],"better":[100],"than":[104],"existing":[105],"estimators,":[107],"such":[108],"as":[109],"coordination":[110],"number,":[111],"half":[112],"sphere":[113],"SphereCon.":[116],"To":[117],"best":[119],"our":[121],"knowledge,":[122],"represents":[124],"first":[126],"estimate":[129],"limited":[135],"model.":[141],"It":[142],"could":[143],"be":[144],"useful":[145],"function":[152],"prediction.":[153],"AVAILABILITYAND":[154],"IMPLEMENTATION:":[155],"free":[159],"available":[160,168],"at":[161,169],"https://github.com/cliffgao/EAGERER.":[162],"SUPPLEMENTARY":[163],"INFORMATION:":[164],"Supplementary":[165],"data":[166],"are":[167],"Bioinformatics":[170],"online.":[171]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}