{"id":"https://openalex.org/W3005012312","doi":"https://doi.org/10.1371/journal.pcbi.1007339","title":"Multi-state design of flexible proteins predicts sequences optimal for conformational change","display_name":"Multi-state design of flexible proteins predicts sequences optimal for conformational change","publication_year":2020,"publication_date":"2020-02-07","ids":{"openalex":"https://openalex.org/W3005012312","doi":"https://doi.org/10.1371/journal.pcbi.1007339","mag":"3005012312","pmid":"https://pubmed.ncbi.nlm.nih.gov/32032348"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007339","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007339","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1007339","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110631998","display_name":"Marion F. Sauer","orcid":null},"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"]},{"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":"Marion F. Sauer","raw_affiliation_strings":["Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America","Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"middle","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"]},{"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":"Alexander M. Sevy","raw_affiliation_strings":["Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America","Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I200719446"]},{"raw_affiliation_string":"Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I901861585"]}]},{"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":["Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America","Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America","Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I901861585"]},{"raw_affiliation_string":"Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America","institution_ids":["https://openalex.org/I901861585"]},{"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"],"affiliations":[{"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":1.4183,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.80853743,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"16","issue":"2","first_page":"e1007339","last_page":"e1007339"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9991000294685364,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/computational-biology","display_name":"Computational biology","score":0.5244213342666626},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.4790452718734741},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.4519698917865753},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.44811636209487915},{"id":"https://openalex.org/keywords/conformational-change","display_name":"Conformational change","score":0.4465036690235138},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38097596168518066},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.34395909309387207},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3070070743560791},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.2947543263435364},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1741454005241394},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.1563408076763153}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5244213342666626},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.4790452718734741},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.4519698917865753},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.44811636209487915},{"id":"https://openalex.org/C2777339483","wikidata":"https://www.wikidata.org/wiki/Q647203","display_name":"Conformational change","level":2,"score":0.4465036690235138},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38097596168518066},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.34395909309387207},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3070070743560791},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.2947543263435364},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1741454005241394},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.1563408076763153}],"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"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}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1007339","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007339","pdf_url":null,"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:32032348","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32032348","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:pcbi00:1007339","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007339","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:b1aa77a247d148a0864db512bb676137","is_oa":true,"landing_page_url":"https://doaj.org/article/b1aa77a247d148a0864db512bb676137","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 16, Iss 2, p e1007339 (2020)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/11824959","is_oa":true,"landing_page_url":"https://figshare.com/articles/Multi-state_design_of_flexible_proteins_predicts_sequences_optimal_for_conformational_change/11824959","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:7032724","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7032724","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007339","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007339","pdf_url":null,"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":[{"score":0.6800000071525574,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G2405216986","display_name":null,"funder_award_id":"U19 AI117905","funder_id":"https://openalex.org/F4320306080","funder_display_name":"Foundation for the National Institutes of Health"},{"id":"https://openalex.org/G3917909134","display_name":null,"funder_award_id":"U19 AI117905","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6286301463","display_name":null,"funder_award_id":"AI117905","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306080","display_name":"Foundation for the National Institutes of Health","ror":"https://ror.org/00k86s890"},{"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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":67,"referenced_works":["https://openalex.org/W836975268","https://openalex.org/W1482971402","https://openalex.org/W1576726980","https://openalex.org/W1968997865","https://openalex.org/W1970858396","https://openalex.org/W1972978214","https://openalex.org/W1978485598","https://openalex.org/W1978763290","https://openalex.org/W1985563952","https://openalex.org/W1988533731","https://openalex.org/W1989368177","https://openalex.org/W1990498887","https://openalex.org/W1990759986","https://openalex.org/W1991917050","https://openalex.org/W1993174731","https://openalex.org/W1997016587","https://openalex.org/W1997477098","https://openalex.org/W2001842251","https://openalex.org/W2005109042","https://openalex.org/W2008545402","https://openalex.org/W2010052045","https://openalex.org/W2037239929","https://openalex.org/W2041404167","https://openalex.org/W2041654633","https://openalex.org/W2042777577","https://openalex.org/W2054467356","https://openalex.org/W2063581254","https://openalex.org/W2063619185","https://openalex.org/W2065921821","https://openalex.org/W2071811516","https://openalex.org/W2074466695","https://openalex.org/W2085075228","https://openalex.org/W2095039045","https://openalex.org/W2096091144","https://openalex.org/W2100733539","https://openalex.org/W2101414350","https://openalex.org/W2106452211","https://openalex.org/W2107867854","https://openalex.org/W2110483430","https://openalex.org/W2124379907","https://openalex.org/W2127322768","https://openalex.org/W2131848438","https://openalex.org/W2142319534","https://openalex.org/W2147098571","https://openalex.org/W2150215096","https://openalex.org/W2158266834","https://openalex.org/W2158492168","https://openalex.org/W2166133396","https://openalex.org/W2168510900","https://openalex.org/W2171641243","https://openalex.org/W2178096376","https://openalex.org/W2201713963","https://openalex.org/W2222445509","https://openalex.org/W2284222372","https://openalex.org/W2302006054","https://openalex.org/W2325963232","https://openalex.org/W2471949356","https://openalex.org/W2557450030","https://openalex.org/W2558409629","https://openalex.org/W2750791471","https://openalex.org/W2767541865","https://openalex.org/W2909279602","https://openalex.org/W2952323901","https://openalex.org/W3128209738","https://openalex.org/W4230413554","https://openalex.org/W4297914773","https://openalex.org/W6648982606"],"related_works":["https://openalex.org/W1988730649","https://openalex.org/W2170120749","https://openalex.org/W2067576503","https://openalex.org/W2199134476","https://openalex.org/W4372348062","https://openalex.org/W2170285690","https://openalex.org/W4390587557","https://openalex.org/W3216044760","https://openalex.org/W2968494487","https://openalex.org/W3180927879"],"abstract_inverted_index":{"Computational":[0],"protein":[1],"design":[2,51],"of":[3,6,22,28,42,47,67,77,109,120,130,152,185,213],"an":[4,150],"ensemble":[5,151],"conformations":[7,43,80,83,153,172],"for":[8],"one":[9],"protein-i.e.,":[10],"multi-state":[11,50],"design-determines":[12],"the":[13,19,29,33,40,45,57,65,97,105,117,128],"side":[14,24,78,219],"chain":[15,25,79,220],"identity":[16],"by":[17,101,167,227],"optimizing":[18],"energetic":[20],"contributions":[21],"that":[23,56,70,138,204],"in":[26,49,92,127,145,191,242],"each":[27],"backbone":[30],"conformations.":[31],"Sampling":[32],"resulting":[34],"large":[35,68],"sequence-structure":[36],"search":[37],"space":[38,99,108],"limits":[39],"number":[41],"and":[44,173,193,244],"size":[46],"proteins":[48,69],"algorithms.":[52],"Here,":[53],"we":[54,136,195],"demonstrated":[55],"REstrained":[58],"CONvergence":[59],"(RECON)":[60],"algorithm":[61],"can":[62],"simultaneously":[63],"evaluate":[64],"sequence":[66,85,98,107,139,192],"undergo":[71],"substantial":[72,143],"conformational":[73,215],"changes.":[74,208],"Simultaneous":[75],"optimization":[76],"across":[81,149],"all":[82,93],"increased":[84,161],"conservation":[86,162],"when":[87,113],"compared":[88],"to":[89,115,157],"single-state":[90],"designs":[91],"cases.":[94],"More":[95],"importantly,":[96],"sampled":[100],"RECON":[102,168],"MSD":[103,169],"resembled":[104],"evolutionary":[106],"flexible":[110],"proteins,":[111],"particularly":[112],"confined":[114],"predicting":[116],"mutational":[118],"preferences":[119],"limited":[121],"common":[122],"ancestral":[123],"descent,":[124],"such":[125,232,239],"as":[126,233,240],"case":[129],"influenza":[131],"type":[132],"A":[133],"hemagglutinin.":[134],"Additionally,":[135],"found":[137],"positions":[140],"which":[141],"require":[142],"changes":[144,216,241],"their":[146],"local":[147,176,218,236],"environment":[148],"are":[154,164],"more":[155],"likely":[156],"be":[158],"conserved.":[159],"These":[160],"rates":[163],"better":[165],"captured":[166,226],"over":[170],"multiple":[171,175],"thus":[174],"residue":[177],"environments":[178],"during":[179],"design.":[180],"To":[181],"quantify":[182],"this":[183],"rewiring":[184],"contacts":[186],"at":[187],"a":[188,197,223],"certain":[189],"position":[190],"structure,":[194],"introduced":[196],"new":[198],"metric":[199],"designated":[200],"'contact":[201],"proximity":[202,221],"deviation'":[203],"enumerates":[205],"contact":[206],"map":[207],"This":[209],"measure":[210],"allows":[211],"mapping":[212],"global":[214,229],"into":[217],"adjustments,":[222],"property":[224],"not":[225],"traditional":[228],"similarity":[230,237],"metrics":[231,238],"RMSD":[234],"or":[235],"\u03c6":[243],"\u03c8":[245],"angles.":[246]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":4}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}