{"id":"https://openalex.org/W4205121726","doi":"https://doi.org/10.1109/bibm52615.2021.9669346","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":2021,"publication_date":"2021-12-09","ids":{"openalex":"https://openalex.org/W4205121726","doi":"https://doi.org/10.1109/bibm52615.2021.9669346"},"language":"en","primary_location":{"id":"doi:10.1109/bibm52615.2021.9669346","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669346","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tiansu Gong","raw_affiliation_strings":["Chinese Academy of Sciences, Key Lab of Intelligent Information Processing, Institute of Computing Technology, Beijing, China","University of Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences, Key Lab of Intelligent Information Processing, Institute of Computing Technology, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"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"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fusong Ju","raw_affiliation_strings":["Chinese Academy of Sciences, Key Lab of Intelligent Information Processing, Institute of Computing Technology, Beijing, China","University of Chinese Academy of Sciences, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences, Key Lab of Intelligent Information Processing, Institute of Computing Technology, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"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"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiwei Sun","raw_affiliation_strings":["Chinese Academy of Sciences, Key Lab of Intelligent Information Processing, Institute of Computing Technology, Beijing, China","University of Chinese Academy of Sciences, Beijing, China","Zhongke Big Data Academy, Zhengzhou, Henan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences, Key Lab of Intelligent Information Processing, Institute of Computing Technology, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Zhongke Big Data Academy, Zhengzhou, Henan, China","institution_ids":[]}]},{"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"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongbo Bu","raw_affiliation_strings":["Chinese Academy of Sciences, Key Lab of Intelligent Information Processing, Institute of Computing Technology, Beijing, China","University of Chinese Academy of Sciences, Beijing, China","Zhongke Big Data Academy, Zhengzhou, Henan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences, Key Lab of Intelligent Information Processing, Institute of Computing Technology, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Zhongke Big Data Academy, Zhengzhou, Henan, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"117","issue":null,"first_page":"32","last_page":"37"},"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":0.998199999332428,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9972000122070312,"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/sasa","display_name":"Sasa","score":0.9086958169937134},{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.6079182624816895},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5900739431381226},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.4375111162662506},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1749797761440277},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08940073847770691},{"id":"https://openalex.org/keywords/geology","display_name":"Geology","score":0.07149839401245117}],"concepts":[{"id":"https://openalex.org/C2776335000","wikidata":"https://www.wikidata.org/wiki/Q2322484","display_name":"Sasa","level":2,"score":0.9086958169937134},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.6079182624816895},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5900739431381226},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.4375111162662506},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1749797761440277},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08940073847770691},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.07149839401245117},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm52615.2021.9669346","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669346","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["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/W2907227701","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/W4385245566","https://openalex.org/W6739901393"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2398796592","https://openalex.org/W4310471119","https://openalex.org/W2280647617","https://openalex.org/W2185678017","https://openalex.org/W2299861993","https://openalex.org/W2190250622","https://openalex.org/W2014342595","https://openalex.org/W2900229032"],"abstract_inverted_index":{"Protein":[0],"structure":[1,50,90,175,180,222],"prediction":[2,29,223],"has":[3],"achieved":[4],"considerable":[5],"progresses":[6],"mainly":[7],"due":[8],"to":[9,147,153,196],"the":[10,18,25,41,53,70,74,92,97,117,159,167,174,185,203],"increased":[11],"accuracy":[12,209],"of":[13,20,24,106,114,120,129,137,212,237],"inter-residue":[14,43,94,205,232],"distance":[15,233],"estimation":[16],"and":[17,45,158,176,198,210,227],"application":[19],"deep":[21,82],"learning":[22],"techniques.Most":[23],"distance-based":[26],"ab":[27],"initio":[28],"approaches":[30,57],"adopt":[31],"a":[32,36,48,81,140,149,179],"two-step":[33],"diagram:":[34],"constructing":[35],"potential":[37,54,76],"function":[38],"based":[39],"on":[40],"estimated":[42,93,160,204],"distances,":[44],"then":[46],"build":[47,200],"3D":[49,89],"that":[51,85,192],"minimizes":[52],"function.":[55],"These":[56],"have":[58],"proven":[59],"very":[60],"promising;":[61],"however,":[62],"they":[63],"still":[64],"suffer":[65],"from":[66,91,202],"several":[67],"limitations,":[68],"especially":[69],"inaccuracies":[71],"incurred":[72],"by":[73],"handcrafted":[75],"function.Here,":[77],"we":[78,190],"present":[79],"SASA-Net,":[80],"learning-based":[83],"approach":[84,99],"directly":[86],"learns":[87],"protein":[88,102,110,221],"distances.":[95,206],"Unlike":[96],"existing":[98],"simply":[100],"representing":[101],"structures":[103,111,201],"as":[104,188],"coordinates":[105],"atoms,":[107],"SASA-Net":[108,138,171,193,213,226,238],"represents":[109],"using":[112],"pose":[113,151],"residues,":[115],"i.e.,":[116],"coordinate":[118],"system":[119],"each":[121],"individual":[122],"residue":[123,131],"in":[124],"which":[125,144],"all":[126,154],"backbone":[127],"atoms":[128],"this":[130],"are":[132],"fixed.":[133],"The":[134,207],"key":[135],"element":[136],"is":[139,145,194,239],"spatial-aware":[141,168],"self-attention":[142,169],"mechanism,":[143,170],"able":[146,195],"adjust":[148],"residue\u2019s":[150],"according":[152],"other":[155],"residues\u2019":[156],"features":[157],"distances":[161],"between":[162],"residues.":[163],"By":[164],"iteratively":[165],"applying":[166],"continuously":[172],"improves":[173],"finally":[177],"acquires":[178],"with":[181],"high":[182,208],"accuracy.":[183],"Using":[184],"CATH35":[186],"proteins":[187],"representatives,":[189],"demonstrate":[191],"accurately":[197],"efficiently":[199],"efficiency":[211],"enables":[214],"an":[215,228],"end-to-end":[216],"neural":[217,229],"network":[218,230],"model":[219],"for":[220,231],"through":[224],"combining":[225],"prediction.":[234],"Source":[235],"code":[236],"available":[240],"at":[241],"https://github.con":[242],"gongtiansu/SASA-Net/":[243]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
