{"id":"https://openalex.org/W836975268","doi":"https://doi.org/10.1371/journal.pcbi.1004300","title":"Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences","display_name":"Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences","publication_year":2015,"publication_date":"2015-07-06","ids":{"openalex":"https://openalex.org/W836975268","doi":"https://doi.org/10.1371/journal.pcbi.1004300","mag":"836975268","pmid":"https://pubmed.ncbi.nlm.nih.gov/26147100"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004300","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004300","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004300&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004300&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056128216","display_name":"Alexander M. Sevy","orcid":"https://orcid.org/0000-0002-2380-2861"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexander M. Sevy","raw_affiliation_strings":["Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I200719446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031485279","display_name":"Timothy M. Jacobs","orcid":"https://orcid.org/0000-0002-1062-2634"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tim M. Jacobs","raw_affiliation_strings":["Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046971682","display_name":"James E. Crowe","orcid":"https://orcid.org/0000-0002-0049-1079"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James E. Crowe","raw_affiliation_strings":["Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025842562","display_name":"Jens Meiler","orcid":"https://orcid.org/0000-0001-8945-193X"},"institutions":[{"id":"https://openalex.org/I200719446","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34","country_code":"US","type":"education","lineage":["https://openalex.org/I200719446"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jens Meiler","raw_affiliation_strings":["Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America; Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America","Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America","Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America; Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America","institution_ids":[]},{"raw_affiliation_string":"Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I200719446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025842562"],"corresponding_institution_ids":["https://openalex.org/I200719446"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.807,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.84459427,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"11","issue":"7","first_page":"e1004300","last_page":"e1004300"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9991999864578247,"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/sequence","display_name":"Sequence (biology)","score":0.7287908792495728},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.6760129928588867},{"id":"https://openalex.org/keywords/convergence","display_name":"Convergence (economics)","score":0.614205539226532},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.5031911730766296},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4936100244522095},{"id":"https://openalex.org/keywords/germline","display_name":"Germline","score":0.49199172854423523},{"id":"https://openalex.org/keywords/protein-engineering","display_name":"Protein engineering","score":0.4906874895095825},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47279661893844604},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.46101441979408264},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.45611923933029175},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3678438067436218},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3251347839832306},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32025614380836487},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.3202306032180786},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.31047672033309937},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27075713872909546},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.15015119314193726},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12719425559043884},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1072947084903717}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7287908792495728},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.6760129928588867},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.614205539226532},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.5031911730766296},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4936100244522095},{"id":"https://openalex.org/C109825262","wikidata":"https://www.wikidata.org/wiki/Q1139164","display_name":"Germline","level":3,"score":0.49199172854423523},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.4906874895095825},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47279661893844604},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.46101441979408264},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.45611923933029175},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3678438067436218},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3251347839832306},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32025614380836487},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3202306032180786},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.31047672033309937},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27075713872909546},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.15015119314193726},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12719425559043884},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1072947084903717},{"id":"https://openalex.org/C50522688","wikidata":"https://www.wikidata.org/wiki/Q189833","display_name":"Economic growth","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"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":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019020","descriptor_name":"Directed Molecular Evolution","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019020","descriptor_name":"Directed Molecular Evolution","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019020","descriptor_name":"Directed Molecular Evolution","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1004300","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004300","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004300&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:26147100","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26147100","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1004300","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004300","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:3b4373d482d64aefa7737b349318d774","is_oa":true,"landing_page_url":"https://doaj.org/article/3b4373d482d64aefa7737b349318d774","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 11, Iss 7, p e1004300 (2015)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3467069","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4493036","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/1475340","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Design_of_Protein_Multi_specificity_Using_an_Independent_Sequence_Search_Reduces_the_Barrier_to_Low_Energy_Sequences_/1475340","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004300","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004300","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004300&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.7900000214576721}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309151","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W836975268.pdf","grobid_xml":"https://content.openalex.org/works/W836975268.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1965802194","https://openalex.org/W1967841473","https://openalex.org/W1969644422","https://openalex.org/W1970858396","https://openalex.org/W1985563952","https://openalex.org/W1987110550","https://openalex.org/W1990498887","https://openalex.org/W1992426410","https://openalex.org/W1993174731","https://openalex.org/W1999749838","https://openalex.org/W2001842251","https://openalex.org/W2002632348","https://openalex.org/W2022231632","https://openalex.org/W2022640182","https://openalex.org/W2026461419","https://openalex.org/W2027662098","https://openalex.org/W2032675793","https://openalex.org/W2035056536","https://openalex.org/W2037511678","https://openalex.org/W2041877620","https://openalex.org/W2041905826","https://openalex.org/W2043883458","https://openalex.org/W2046994420","https://openalex.org/W2054467356","https://openalex.org/W2058001460","https://openalex.org/W2066381187","https://openalex.org/W2067576503","https://openalex.org/W2071811516","https://openalex.org/W2080057469","https://openalex.org/W2081926288","https://openalex.org/W2084493621","https://openalex.org/W2094392347","https://openalex.org/W2095039045","https://openalex.org/W2103622571","https://openalex.org/W2107903949","https://openalex.org/W2111936772","https://openalex.org/W2135815512","https://openalex.org/W2137015675","https://openalex.org/W2137054136","https://openalex.org/W2147951465","https://openalex.org/W2152617913","https://openalex.org/W2155432846","https://openalex.org/W2158714788","https://openalex.org/W2159247900","https://openalex.org/W2164958220","https://openalex.org/W2168510900","https://openalex.org/W2201713963","https://openalex.org/W2222445509","https://openalex.org/W4230932396","https://openalex.org/W4239206225","https://openalex.org/W6663958344"],"related_works":["https://openalex.org/W2554214300","https://openalex.org/W2116266427","https://openalex.org/W2991041010","https://openalex.org/W2003675367","https://openalex.org/W2991203454","https://openalex.org/W2512252615","https://openalex.org/W2409023191","https://openalex.org/W1988730649","https://openalex.org/W2901595550","https://openalex.org/W4214858168"],"abstract_inverted_index":{"Computational":[0],"protein":[1,38,134,201],"design":[2,22,26,57,71,142,168],"has":[3],"found":[4],"great":[5],"success":[6],"in":[7,18,55,129,196],"engineering":[8],"proteins":[9,171],"for":[10,95],"thermodynamic":[11],"stability,":[12],"binding":[13,174],"specificity,":[14],"or":[15],"enzymatic":[16],"activity":[17],"a":[19,44,76,84,122,132,150],"'single":[20],"state'":[21],"(SSD)":[23],"paradigm.":[24],"Multi-specificity":[25],"(MSD),":[27],"on":[28,79,108,140],"the":[29,34,70,111,118,162,180],"other":[30],"hand,":[31],"involves":[32],"considering":[33],"stability":[35],"of":[36,161,179,200],"multiple":[37],"states":[39,110],"simultaneously.":[40],"We":[41,136,183],"have":[42,137],"developed":[43],"novel":[45],"MSD":[46,100],"algorithm,":[47],"which":[48,116],"we":[49,145,167],"refer":[50],"to":[51,64,83,99,158,189],"as":[52],"REstrained":[53],"CONvergence":[54],"multi-specificity":[56],"(RECON).":[58],"The":[59],"algorithm":[60],"allows":[61],"each":[62],"state":[63],"adopt":[65],"its":[66],"own":[67],"sequence":[68,78,86,107],"throughout":[69],"process":[72],"rather":[73],"than":[74],"enforcing":[75],"single":[77,85],"all":[80,109,173],"states.":[81],"Convergence":[82],"is":[87,114,187],"encouraged":[88],"through":[89],"an":[90,105],"incrementally":[91],"increasing":[92],"convergence":[93],"restraint":[94],"corresponding":[96],"positions.":[97],"Compared":[98],"algorithms":[101],"that":[102,185],"enforce":[103],"(constrain)":[104],"identical":[106],"energy":[112],"landscape":[113],"simplified,":[115],"accelerates":[117],"search":[119],"drastically.":[120],"As":[121],"result,":[123],"RECON":[124,139,186],"can":[125],"readily":[126],"be":[127],"used":[128],"simulations":[130],"with":[131],"flexible":[133],"backbone.":[135],"benchmarked":[138],"two":[141],"tasks.":[143],"First,":[144],"designed":[146],"antibodies":[147],"derived":[148],"from":[149],"common":[151],"germline":[152],"gene":[153],"against":[154,172],"their":[155],"diverse":[156,198],"targets":[157],"assess":[159],"recovery":[160,178],"germline,":[163],"polyspecific":[164,170],"sequence.":[165,182],"Second,":[166],"\"promiscuous\",":[169],"partners":[175],"and":[176],"measure":[177],"native":[181],"show":[184],"able":[188],"efficiently":[190],"recover":[191],"native-like,":[192],"biologically":[193],"relevant":[194],"sequences":[195],"this":[197],"set":[199],"complexes.":[202]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
