{"id":"https://openalex.org/W4309097826","doi":"https://doi.org/10.1093/bioinformatics/btac733","title":"Deep learning of protein sequence design of protein\u2013protein interactions","display_name":"Deep learning of protein sequence design of protein\u2013protein interactions","publication_year":2022,"publication_date":"2022-11-15","ids":{"openalex":"https://openalex.org/W4309097826","doi":"https://doi.org/10.1093/bioinformatics/btac733","pmid":"https://pubmed.ncbi.nlm.nih.gov/36377772"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac733","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac733","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac733/48448882/btac733.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac733/48448882/btac733.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071572776","display_name":"Raulia Syrlybaeva","orcid":null},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Raulia Syrlybaeva","raw_affiliation_strings":["Department of Pharmaceutical and Biomedical Sciences, University of Georgia , Athens, GA 30602, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical and Biomedical Sciences, University of Georgia , Athens, GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011133927","display_name":"Eva\u2010Maria Strauch","orcid":"https://orcid.org/0000-0001-7382-747X"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eva-Maria Strauch","raw_affiliation_strings":["Department of Pharmaceutical and Biomedical Sciences, University of Georgia , Athens, GA 30602, USA","Institute of Bioinformatics, University of Georgia , Athens, GA 30602, USA"],"raw_orcid":"https://orcid.org/0000-0001-7382-747X","affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical and Biomedical Sciences, University of Georgia , Athens, GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Institute of Bioinformatics, University of Georgia , Athens, GA 30602, USA","institution_ids":["https://openalex.org/I165733156"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5011133927"],"corresponding_institution_ids":["https://openalex.org/I165733156"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2556,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.79004411,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.415800005197525,"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":0.415800005197525,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.31610000133514404,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.07509999722242355,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.6979550123214722},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.6000121235847473},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5429761409759521},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5184118747711182},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4937461316585541},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.3983728587627411},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3977551758289337},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3097212016582489},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.24802851676940918},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24291753768920898},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14258480072021484}],"concepts":[{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.6979550123214722},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.6000121235847473},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5429761409759521},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5184118747711182},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4937461316585541},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3983728587627411},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3977551758289337},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3097212016582489},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.24802851676940918},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24291753768920898},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14258480072021484}],"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":"D000077321","descriptor_name":"Deep Learning","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":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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":null,"qualifier_name":null,"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac733","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac733","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac733/48448882/btac733.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36377772","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36377772","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},{"id":"pmh:oai:pubmedcentral.nih.gov:9947925","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9947925","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac733","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac733","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac733/48448882/btac733.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4181737118","display_name":"Design of Antivirals and Immunogens Targeting Paramyxoviruses","funder_award_id":"5r01ai140245-05","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G964564425","display_name":null,"funder_award_id":"R01-AI140245","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4309097826.pdf","grobid_xml":"https://content.openalex.org/works/W4309097826.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1975837892","https://openalex.org/W1985907120","https://openalex.org/W1992450378","https://openalex.org/W1999390565","https://openalex.org/W1999648327","https://openalex.org/W2002632348","https://openalex.org/W2022781946","https://openalex.org/W2031132894","https://openalex.org/W2034326919","https://openalex.org/W2035942032","https://openalex.org/W2039928024","https://openalex.org/W2043284163","https://openalex.org/W2053134976","https://openalex.org/W2058527555","https://openalex.org/W2077219861","https://openalex.org/W2129138941","https://openalex.org/W2130479394","https://openalex.org/W2135815512","https://openalex.org/W2148895983","https://openalex.org/W2345741266","https://openalex.org/W2519539312","https://openalex.org/W2790952361","https://openalex.org/W2886156472","https://openalex.org/W2908391177","https://openalex.org/W2908544250","https://openalex.org/W2953176058","https://openalex.org/W2970594786","https://openalex.org/W2991877021","https://openalex.org/W2992070886","https://openalex.org/W2993355183","https://openalex.org/W2995570577","https://openalex.org/W2997244915","https://openalex.org/W2999044305","https://openalex.org/W3084236163","https://openalex.org/W3085631952","https://openalex.org/W3087602797","https://openalex.org/W3090060810","https://openalex.org/W3096331199","https://openalex.org/W3100159300","https://openalex.org/W3164039183","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3207204660","https://openalex.org/W4210861939","https://openalex.org/W4220765272","https://openalex.org/W4220851837"],"related_works":["https://openalex.org/W2053028024","https://openalex.org/W2170120749","https://openalex.org/W4281626490","https://openalex.org/W2011602722","https://openalex.org/W2067576503","https://openalex.org/W2199134476","https://openalex.org/W2997244915","https://openalex.org/W2170285690","https://openalex.org/W1988730649","https://openalex.org/W4387310732"],"abstract_inverted_index":{"MOTIVATION:":[0],"As":[1],"more":[2,20],"data":[3,162],"of":[4,30,82,143,152],"experimentally":[5],"determined":[6],"protein":[7,16,70,84,89],"structures":[8],"are":[9,163],"becoming":[10],"available,":[11],"data-driven":[12],"models":[13],"to":[14,47,66],"describe":[15],"sequence-structure":[17],"relationships":[18],"become":[19],"feasible.":[21],"Within":[22],"this":[23],"space,":[24],"the":[25,80,87,95,153],"amino":[26],"acid":[27],"sequence":[28],"design":[29,67,142],"protein-protein":[31,101,144],"interactions":[32,102,113],"is":[33,45,155],"still":[34],"a":[35,128],"rather":[36],"challenging":[37],"subproblem":[38],"with":[39,139],"very":[40],"low":[41],"success":[42],"rates-yet,":[43],"it":[44,133],"central":[46],"most":[48],"biological":[49],"processes.":[50],"RESULTS:":[51],"We":[52],"developed":[53],"an":[54,134],"attention-based":[55],"deep":[56],"learning":[57],"model":[58,75,124],"inspired":[59],"by":[60,97],"algorithms":[61],"used":[62],"for":[63,79,137],"image-caption":[64],"assignments":[65],"peptides":[68],"or":[69,86],"fragment":[71],"sequences.":[72],"Our":[73],"trained":[74],"can":[76],"be":[77],"applied":[78],"redesign":[81],"natural":[83],"interfaces":[85,108],"designed":[88,107],"interaction":[90],"fragments.":[91],"Here,":[92],"we":[93],"validate":[94],"potential":[96],"recapitulating":[98],"naturally":[99],"occurring":[100],"including":[103],"antibody-antigen":[104],"complexes.":[105],"The":[106,149],"accurately":[109],"capture":[110],"essential":[111],"native":[112],"and":[114],"have":[115],"comparable":[116],"native-like":[117],"binding":[118],"affinities":[119],"in":[120],"silico.":[121],"Furthermore,":[122],"our":[123],"does":[125],"not":[126],"need":[127],"precise":[129],"backbone":[130],"location,":[131],"making":[132],"attractive":[135],"tool":[136],"working":[138],"de":[140],"novo":[141],"interactions.":[145],"AVAILABILITY":[146],"AND":[147],"IMPLEMENTATION:":[148],"source":[150],"code":[151],"method":[154],"available":[156,164],"at":[157,165],"https://github.com/strauchlab/iNNterfaceDesign.":[158],"SUPPLEMENTARY":[159],"INFORMATION:":[160],"Supplementary":[161],"Bioinformatics":[166],"online.":[167]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":6}],"updated_date":"2026-08-08T07:41:36.138363","created_date":"2025-10-10T00:00:00"}
