{"id":"https://openalex.org/W4299497354","doi":"https://doi.org/10.1109/tcbb.2022.3197802","title":"ContactLib-ATT: A Structure-Based Search Engine for Homologous Proteins","display_name":"ContactLib-ATT: A Structure-Based Search Engine for Homologous Proteins","publication_year":2022,"publication_date":"2022-08-10","ids":{"openalex":"https://openalex.org/W4299497354","doi":"https://doi.org/10.1109/tcbb.2022.3197802","pmid":"https://pubmed.ncbi.nlm.nih.gov/35947567"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2022.3197802","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3197802","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/A5103175794","display_name":"Cheng Chen","orcid":"https://orcid.org/0000-0003-1460-6997"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Cheng Chen","raw_affiliation_strings":["School of Computer Science and Technology, Shandong University, Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0003-1460-6997","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055014462","display_name":"Yuguo Zha","orcid":"https://orcid.org/0000-0003-3702-9416"},"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":"Yuguo Zha","raw_affiliation_strings":["College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101769221","display_name":"Daming Zhu","orcid":"https://orcid.org/0000-0001-9395-7247"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Daming Zhu","raw_affiliation_strings":["School of Computer Science and Technology, Shandong University, Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0001-9395-7247","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076346443","display_name":"Kang Ning","orcid":"https://orcid.org/0000-0003-3325-5387"},"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":"Kang Ning","raw_affiliation_strings":["College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101906222","display_name":"Xuefeng Cui","orcid":"https://orcid.org/0000-0002-8816-3482"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuefeng Cui","raw_affiliation_strings":["School of Computer Science and Technology, Shandong University, Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0002-8816-3482","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5103175794"],"corresponding_institution_ids":["https://openalex.org/I80143920"],"apc_list":null,"apc_paid":null,"fwci":0.2604,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.52608835,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"20","issue":"6","first_page":"3421","last_page":"3429"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9961000084877014,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9958999752998352,"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/embedding","display_name":"Embedding","score":0.8530533313751221},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6258957386016846},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5743604898452759},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5531187057495117},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.4612514078617096},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4581427276134491},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4542374014854431},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.44639265537261963},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4416351318359375},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39241641759872437},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3430324196815491},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14813032746315002},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07812705636024475},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0700472891330719}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.8530533313751221},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6258957386016846},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5743604898452759},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5531187057495117},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.4612514078617096},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4581427276134491},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4542374014854431},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.44639265537261963},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4416351318359375},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39241641759872437},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3430324196815491},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14813032746315002},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07812705636024475},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0700472891330719},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057386","descriptor_name":"Search Engine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2022.3197802","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2022.3197802","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:35947567","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35947567","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":[{"display_name":"Partnerships for the goals","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G1729077721","display_name":null,"funder_award_id":"61732009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4052770625","display_name":null,"funder_award_id":"32071465","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4196378014","display_name":null,"funder_award_id":"31671374","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6392341960","display_name":null,"funder_award_id":"31871334","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7587655767","display_name":null,"funder_award_id":"62072283","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7981141699","display_name":null,"funder_award_id":"2018YFC0910502","funder_id":"https://openalex.org/F4320322108","funder_display_name":"Ministry of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322108","display_name":"Ministry of Science and Technology","ror":"https://ror.org/032e49973"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1514151181","https://openalex.org/W1904365287","https://openalex.org/W1916412816","https://openalex.org/W1917981667","https://openalex.org/W2008708467","https://openalex.org/W2009247363","https://openalex.org/W2072404529","https://openalex.org/W2074231493","https://openalex.org/W2090617952","https://openalex.org/W2099946731","https://openalex.org/W2102245393","https://openalex.org/W2102856132","https://openalex.org/W2106433904","https://openalex.org/W2115540209","https://openalex.org/W2116341502","https://openalex.org/W2130479394","https://openalex.org/W2131410522","https://openalex.org/W2135621733","https://openalex.org/W2137955461","https://openalex.org/W2144998676","https://openalex.org/W2145268834","https://openalex.org/W2157965775","https://openalex.org/W2161072217","https://openalex.org/W2161151688","https://openalex.org/W2161311439","https://openalex.org/W2792643794","https://openalex.org/W2889085087","https://openalex.org/W2898364362","https://openalex.org/W2900701906","https://openalex.org/W2902353954","https://openalex.org/W2909727437","https://openalex.org/W2949985837","https://openalex.org/W2950806586","https://openalex.org/W2953360940","https://openalex.org/W2963173418","https://openalex.org/W2973105562","https://openalex.org/W3016492430","https://openalex.org/W3037888463","https://openalex.org/W3094502228","https://openalex.org/W3101509328","https://openalex.org/W3108721542","https://openalex.org/W3115809040","https://openalex.org/W3119872582","https://openalex.org/W3146944767","https://openalex.org/W3152893301","https://openalex.org/W4205395213","https://openalex.org/W4255594044","https://openalex.org/W6640036494","https://openalex.org/W6683965311","https://openalex.org/W6739901393","https://openalex.org/W6749029207","https://openalex.org/W6749107692","https://openalex.org/W6757712183","https://openalex.org/W6758485811","https://openalex.org/W6763509872","https://openalex.org/W6765474767","https://openalex.org/W6780226713","https://openalex.org/W6784333009"],"related_works":["https://openalex.org/W2081900870","https://openalex.org/W2181948922","https://openalex.org/W2384362569","https://openalex.org/W2183306018","https://openalex.org/W2549990292","https://openalex.org/W2345479200","https://openalex.org/W4205302943","https://openalex.org/W2951819827","https://openalex.org/W2119949815","https://openalex.org/W2932872266"],"abstract_inverted_index":{"General-purpose":[0],"protein":[1,10,15,48,83],"structure":[2,49,84],"embedding":[3,50,57,69,85],"can":[4],"be":[5],"used":[6,120],"for":[7,76,127],"many":[8],"important":[9],"biology":[11],"tasks,":[12],"such":[13],"as":[14],"design,":[16],"drug":[17],"design":[18],"and":[19,89,131],"binding":[20],"affinity":[21],"prediction.":[22],"Recent":[23],"researches":[24],"have":[25],"shown":[26],"that":[27],"attention-based":[28,71],"encoder":[29,72],"layers":[30,73],"are":[31,74],"more":[32,61],"suitable":[33],"to":[34,121],"learn":[35],"high-level":[36],"features.":[37],"Based":[38],"on":[39,91],"this":[40],"key":[41],"observation,":[42],"we":[43],"propose":[44],"a":[45,59,97,101,123,143],"two-level":[46],"general-purpose":[47,82],"neural":[51],"network,":[52],"called":[53],"ContactLib-ATT.":[54],"On":[55,67,114],"local":[56],"level,":[58,70],"biologically":[60],"meaningful":[62],"contact":[63],"context":[64],"is":[65,87,119],"introduced.":[66],"global":[68,78],"employed":[75],"better":[77],"representation":[79],"learning.":[80],"Our":[81],"framework":[86],"trained":[88],"tested":[90],"the":[92,115],"SCOP40":[93],"2.07":[94],"dataset.":[95],"As":[96],"result,":[98],"ContactLib-ATT":[99,118],"achieves":[100],"SCOP":[102],"superfamily":[103],"classification":[104],"accuracy":[105],"of":[106,145],"82.4%":[107],"(i.e.,":[108],"6.7%":[109],"higher":[110],"than":[111],"state-of-the-art":[112],"method).":[113],"same":[116],"dataset,":[117],"simulate":[122],"structure-based":[124],"search":[125],"engine":[126],"remote":[128,140],"homologous":[129],"proteins,":[130],"our":[132],"top-10":[133],"candidate":[134],"list":[135],"contains":[136],"at":[137],"least":[138],"one":[139],"homolog":[141],"with":[142],"probability":[144],"91.9%.":[146]},"counts_by_year":[{"year":2025,"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"}
