{"id":"https://openalex.org/W4320015740","doi":"https://doi.org/10.1109/tcbb.2023.3240456","title":"SASA-Net: A Spatial-Aware Self-Attention Mechanism for Building Protein 3D Structure Directly From Inter- Residue Distances","display_name":"SASA-Net: A Spatial-Aware Self-Attention Mechanism for Building Protein 3D Structure Directly From Inter- Residue Distances","publication_year":2023,"publication_date":"2023-01-30","ids":{"openalex":"https://openalex.org/W4320015740","doi":"https://doi.org/10.1109/tcbb.2023.3240456","pmid":"https://pubmed.ncbi.nlm.nih.gov/37022274"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2023.3240456","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3240456","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM Transactions on Computational Biology and Bioinformatics","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/A5013149416","display_name":"Tiansu Gong","orcid":"https://orcid.org/0000-0003-1407-5882"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tiansu Gong","raw_affiliation_strings":["Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0003-1407-5882","affiliations":[{"raw_affiliation_string":"Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020656041","display_name":"Fusong Ju","orcid":"https://orcid.org/0000-0002-0467-7858"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fusong Ju","raw_affiliation_strings":["Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108903761","display_name":"Shiwei Sun","orcid":"https://orcid.org/0000-0002-0351-3720"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiwei Sun","raw_affiliation_strings":["Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076729236","display_name":"Dongbo Bu","orcid":"https://orcid.org/0000-0003-4119-4238"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongbo Bu","raw_affiliation_strings":["Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4036,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.63790936,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"6","first_page":"3482","last_page":"3488"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9962999820709229,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9951000213623047,"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/sasa","display_name":"Sasa","score":0.9706590175628662},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.633473813533783},{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.5922887325286865},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.540741503238678},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4723031520843506},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45928052067756653},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.41370129585266113},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.14537781476974487},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.06928360462188721}],"concepts":[{"id":"https://openalex.org/C2776335000","wikidata":"https://www.wikidata.org/wiki/Q2322484","display_name":"Sasa","level":2,"score":0.9706590175628662},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.633473813533783},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.5922887325286865},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.540741503238678},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4723031520843506},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45928052067756653},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.41370129585266113},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.14537781476974487},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.06928360462188721},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2023.3240456","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3240456","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37022274","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37022274","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/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1887041509","display_name":null,"funder_award_id":"32271297","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4314963621","display_name":null,"funder_award_id":"62072435","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7924934264","display_name":null,"funder_award_id":"82130055","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G975092767","display_name":null,"funder_award_id":"2020YFA0907000","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1491063910","https://openalex.org/W1976666280","https://openalex.org/W1979762151","https://openalex.org/W1987134040","https://openalex.org/W2014050554","https://openalex.org/W2037312364","https://openalex.org/W2065921821","https://openalex.org/W2558272290","https://openalex.org/W2949867299","https://openalex.org/W2967606876","https://openalex.org/W2968494487","https://openalex.org/W2997234557","https://openalex.org/W2999044305","https://openalex.org/W3157271872","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W6739901393"],"related_works":["https://openalex.org/W2946599741","https://openalex.org/W2593264178","https://openalex.org/W2043066834","https://openalex.org/W3171039768","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2058542300","https://openalex.org/W1564749278","https://openalex.org/W2294851134","https://openalex.org/W3215498386"],"abstract_inverted_index":{"Protein":[0],"functions":[1],"are":[2,20,158],"tightly":[3],"related":[4],"to":[5,33,173,179,222],"the":[6,34,42,50,66,78,95,99,118,123,143,185,193,200,211,229],"fine":[7],"details":[8],"of":[9,37,44,49,132,140,146,155,163,238,263],"their":[10],"3D":[11,74,115],"structures.":[12],"To":[13],"understand":[14],"protein":[15,24,114,128,136,247],"structures,":[16],"computational":[17],"prediction":[18,26,54,249],"approaches":[19,55,82],"highly":[21],"needed.":[22],"Recently,":[23],"structure":[25,75,116,201,206,248],"has":[27],"achieved":[28],"considerable":[29],"progresses":[30],"mainly":[31],"due":[32],"increased":[35],"accuracy":[36,235],"inter-residue":[38,68,120,231,258],"distance":[39,259],"estimation":[40],"and":[41,70,184,202,224,236,253],"application":[43],"deep":[45,108],"learning":[46],"techniques.":[47],"Most":[48],"distance-based":[51],"ab":[52],"initio":[53],"adopt":[56],"a":[57,61,73,107,166,175,205],"two-step":[58],"diagram:":[59],"constructing":[60],"potential":[62,79,101],"function":[63],"based":[64],"on":[65],"estimated":[67,119,186,230],"distances,":[69],"then":[71],"build":[72,226],"that":[76,111,218],"minimizes":[77],"function.":[80,102],"These":[81],"have":[83],"proven":[84],"very":[85],"promising;":[86],"however,":[87],"they":[88],"still":[89],"suffer":[90],"from":[91,117,228],"several":[92],"limitations,":[93],"especially":[94],"inaccuracies":[96],"incurred":[97],"by":[98],"handcrafted":[100],"Here,":[103],"we":[104,216],"present":[105],"SASA-Net,":[106],"learning-based":[109],"approach":[110,125],"directly":[112],"learns":[113],"distances.":[121,232],"Unlike":[122],"existing":[124],"simply":[126],"representing":[127],"structures":[129,137,227],"as":[130,214],"coordinates":[131],"atoms,":[133],"SASA-Net":[134,164,197,219,239,252,264],"represents":[135],"using":[138],"pose":[139,177],"residues,":[141],"i.e.,":[142],"coordinate":[144],"system":[145],"each":[147],"individual":[148],"residue":[149,157],"in":[150],"which":[151,170],"all":[152,180],"backbone":[153],"atoms":[154],"this":[156],"fixed.":[159],"The":[160,233],"key":[161],"element":[162],"is":[165,171,220,265],"spatial-aware":[167,194],"self-attention":[168,195],"mechanism,":[169,196],"able":[172,221],"adjust":[174],"residue's":[176],"according":[178],"other":[181],"residues'":[182],"features":[183],"distances":[187],"between":[188],"residues.":[189],"By":[190],"iteratively":[191],"applying":[192],"continuously":[198],"improves":[199],"finally":[203],"acquires":[204],"with":[207],"high":[208,234],"accuracy.":[209],"Using":[210],"CATH35":[212],"proteins":[213],"representatives,":[215],"demonstrate":[217],"accurately":[223],"efficiently":[225],"efficiency":[237],"enables":[240],"an":[241,254],"end-to-end":[242],"neural":[243,255],"network":[244,256],"model":[245],"for":[246,257],"through":[250],"combining":[251],"prediction.":[260],"Source":[261],"code":[262],"available":[266],"at":[267],"https://github.com/gongtiansu/SASA-Net/.":[268]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
