{"id":"https://openalex.org/W3033967289","doi":"https://doi.org/10.1371/journal.pcbi.1007447","title":"Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface","display_name":"Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface","publication_year":2020,"publication_date":"2020-06-08","ids":{"openalex":"https://openalex.org/W3033967289","doi":"https://doi.org/10.1371/journal.pcbi.1007447","mag":"3033967289","pmid":"https://pubmed.ncbi.nlm.nih.gov/32511232"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007447","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007447","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007447&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.1007447&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033672307","display_name":"Anna U. Lowegard","orcid":"https://orcid.org/0000-0002-1259-2790"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]},{"id":"https://openalex.org/I4210126298","display_name":"Duke Medical Center","ror":"https://ror.org/03njmea73","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876"]},{"id":"https://openalex.org/I4210153043","display_name":"Duke University Hospital","ror":"https://ror.org/04bct7p84","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876","https://openalex.org/I4210144876","https://openalex.org/I4210153043"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anna U. Lowegard","raw_affiliation_strings":["Department of Computer Science, Duke University, Durham, North Carolina, United States of America","Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-1259-2790","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University, Durham, North Carolina, United States of America","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America","institution_ids":["https://openalex.org/I170897317","https://openalex.org/I4210153043","https://openalex.org/I4210126298"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024660770","display_name":"Marcel S. Frenkel","orcid":"https://orcid.org/0000-0002-5638-7692"},"institutions":[{"id":"https://openalex.org/I4210126298","display_name":"Duke Medical Center","ror":"https://ror.org/03njmea73","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marcel S. Frenkel","raw_affiliation_strings":["Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-5638-7692","affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America","institution_ids":["https://openalex.org/I4210126298"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019160089","display_name":"Graham T. Holt","orcid":"https://orcid.org/0000-0003-3354-9748"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]},{"id":"https://openalex.org/I4210126298","display_name":"Duke Medical Center","ror":"https://ror.org/03njmea73","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876"]},{"id":"https://openalex.org/I4210153043","display_name":"Duke University Hospital","ror":"https://ror.org/04bct7p84","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876","https://openalex.org/I4210144876","https://openalex.org/I4210153043"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Graham T. Holt","raw_affiliation_strings":["Department of Computer Science, Duke University, Durham, North Carolina, United States of America","Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University, Durham, North Carolina, United States of America","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America","institution_ids":["https://openalex.org/I170897317","https://openalex.org/I4210153043","https://openalex.org/I4210126298"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011039716","display_name":"Jonathan Jou","orcid":"https://orcid.org/0000-0001-7172-9032"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan D. Jou","raw_affiliation_strings":["Department of Computer Science, Duke University, Durham, North Carolina, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-7172-9032","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University, Durham, North Carolina, United States of America","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012624311","display_name":"Adegoke A. Ojewole","orcid":"https://orcid.org/0000-0003-2661-4388"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]},{"id":"https://openalex.org/I4210126298","display_name":"Duke Medical Center","ror":"https://ror.org/03njmea73","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876"]},{"id":"https://openalex.org/I4210153043","display_name":"Duke University Hospital","ror":"https://ror.org/04bct7p84","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876","https://openalex.org/I4210144876","https://openalex.org/I4210153043"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adegoke A. Ojewole","raw_affiliation_strings":["Department of Computer Science, Duke University, Durham, North Carolina, United States of America","Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-2661-4388","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University, Durham, North Carolina, United States of America","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Program in Computational Biology and Bioinformatics, Duke University Medical Center, Durham, North Carolina, United States of America","institution_ids":["https://openalex.org/I170897317","https://openalex.org/I4210153043","https://openalex.org/I4210126298"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046723017","display_name":"Bruce R. Donald","orcid":"https://orcid.org/0000-0001-6884-4398"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]},{"id":"https://openalex.org/I4210126298","display_name":"Duke Medical Center","ror":"https://ror.org/03njmea73","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210126298","https://openalex.org/I4210144876"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bruce R. Donald","raw_affiliation_strings":["Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America","Department of Computer Science, Duke University, Durham, North Carolina, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, United States of America","institution_ids":["https://openalex.org/I4210126298"]},{"raw_affiliation_string":"Department of Computer Science, Duke University, Durham, North Carolina, United States of America","institution_ids":["https://openalex.org/I170897317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5046723017"],"corresponding_institution_ids":["https://openalex.org/I170897317","https://openalex.org/I4210126298"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.0032,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.74694126,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"16","issue":"6","first_page":"e1007447","last_page":"e1007447"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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":0.9990000128746033,"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":0.9970999956130981,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.9962999820709229,"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/protein-design","display_name":"Protein design","score":0.7722733020782471},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6561971306800842},{"id":"https://openalex.org/keywords/partition","display_name":"Partition (number theory)","score":0.5506731867790222},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5431311726570129},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5384544730186462},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.5328885316848755},{"id":"https://openalex.org/keywords/partition-function","display_name":"Partition function (quantum field theory)","score":0.4245389699935913},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3514575660228729},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.30705034732818604},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.29939961433410645},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.19341695308685303},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.13349604606628418},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11551705002784729},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09345054626464844}],"concepts":[{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.7722733020782471},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6561971306800842},{"id":"https://openalex.org/C42812","wikidata":"https://www.wikidata.org/wiki/Q1082910","display_name":"Partition (number theory)","level":2,"score":0.5506731867790222},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5431311726570129},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5384544730186462},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.5328885316848755},{"id":"https://openalex.org/C2778401447","wikidata":"https://www.wikidata.org/wiki/Q7140637","display_name":"Partition function (quantum field theory)","level":2,"score":0.4245389699935913},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3514575660228729},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.30705034732818604},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.29939961433410645},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.19341695308685303},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.13349604606628418},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11551705002784729},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09345054626464844},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","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":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007368","descriptor_name":"Interferometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007368","descriptor_name":"Interferometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007368","descriptor_name":"Interferometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"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":"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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016283","descriptor_name":"Proto-Oncogene Proteins p21(ras)","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016283","descriptor_name":"Proto-Oncogene Proteins p21(ras)","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016283","descriptor_name":"Proto-Oncogene Proteins p21(ras)","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019908","descriptor_name":"Proto-Oncogene Proteins c-raf","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019908","descriptor_name":"Proto-Oncogene Proteins c-raf","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019908","descriptor_name":"Proto-Oncogene Proteins c-raf","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D037102","descriptor_name":"Lectins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D037102","descriptor_name":"Lectins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D037102","descriptor_name":"Lectins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1007447","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007447","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007447&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:32511232","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32511232","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:pcbi00:1007447","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007447","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:f824df9242644807b55d5143527212cf","is_oa":true,"landing_page_url":"https://doaj.org/article/f824df9242644807b55d5143527212cf","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 6, p e1007447 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7329130","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7329130","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007447","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007447","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007447&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":[{"score":0.8199999928474426,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G3914163144","display_name":null,"funder_award_id":"R01-GM078031","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6873007563","display_name":null,"funder_award_id":"R01-GM118543","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306799","display_name":"Pharmaceutical Research and Manufacturers of America Foundation","ror":"https://ror.org/01z88k350"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3033967289.pdf","grobid_xml":"https://content.openalex.org/works/W3033967289.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W1511802341","https://openalex.org/W1579246604","https://openalex.org/W1606858778","https://openalex.org/W1721447212","https://openalex.org/W1813117265","https://openalex.org/W1953264505","https://openalex.org/W1965800930","https://openalex.org/W1966185591","https://openalex.org/W1971102429","https://openalex.org/W1974647057","https://openalex.org/W1980703922","https://openalex.org/W1981699164","https://openalex.org/W1982813290","https://openalex.org/W1987365716","https://openalex.org/W1987977716","https://openalex.org/W1993202007","https://openalex.org/W1999068679","https://openalex.org/W2009239521","https://openalex.org/W2012575827","https://openalex.org/W2012987401","https://openalex.org/W2017829285","https://openalex.org/W2022643782","https://openalex.org/W2031195527","https://openalex.org/W2034882714","https://openalex.org/W2041638382","https://openalex.org/W2042855904","https://openalex.org/W2045023379","https://openalex.org/W2049815423","https://openalex.org/W2051576153","https://openalex.org/W2071337276","https://openalex.org/W2073125464","https://openalex.org/W2075597039","https://openalex.org/W2076261991","https://openalex.org/W2085497102","https://openalex.org/W2096648003","https://openalex.org/W2097649955","https://openalex.org/W2097669648","https://openalex.org/W2108422942","https://openalex.org/W2109948087","https://openalex.org/W2126296369","https://openalex.org/W2128831799","https://openalex.org/W2135815512","https://openalex.org/W2138309709","https://openalex.org/W2139827114","https://openalex.org/W2141612292","https://openalex.org/W2141795045","https://openalex.org/W2145898846","https://openalex.org/W2150155770","https://openalex.org/W2157650375","https://openalex.org/W2162292142","https://openalex.org/W2164932718","https://openalex.org/W2172114588","https://openalex.org/W2173184980","https://openalex.org/W2201713963","https://openalex.org/W2252678535","https://openalex.org/W2321693457","https://openalex.org/W2328911273","https://openalex.org/W2340987618","https://openalex.org/W2378386504","https://openalex.org/W2401119760","https://openalex.org/W2507985331","https://openalex.org/W2528831027","https://openalex.org/W2557731087","https://openalex.org/W2559476455","https://openalex.org/W2607270245","https://openalex.org/W2734828379","https://openalex.org/W2751676477","https://openalex.org/W2884472827","https://openalex.org/W2903703987","https://openalex.org/W2919751133","https://openalex.org/W2951122824","https://openalex.org/W2995121092","https://openalex.org/W4230223507","https://openalex.org/W4246464108"],"related_works":["https://openalex.org/W4294567731","https://openalex.org/W2808407214","https://openalex.org/W2170120749","https://openalex.org/W4281626490","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":{"The":[0,245],"K*":[1,110],"algorithm":[2],"provably":[3,153],"approximates":[4],"partition":[5,32,169],"functions":[6,33],"for":[7,27,57,184,306,393],"a":[8,19,28,35,61,83,105,217,226,261,311,345,378],"set":[9,30],"of":[10,31,38,45,64,147,219,228,241,248,259,273,277,282,318,348,375,438],"states":[11],"(e.g.,":[12],"protein,":[13],"ligand,":[14],"and":[15,40,68,137,163,206,216,309,383,417,436,453],"protein-ligand":[16],"complex)":[17],"to":[18,74,81,85,120,172,191,195,235,320,343],"user-specified":[20,106],"accuracy":[21,156],"\u03b5.":[22],"Often,":[23],"reaching":[24],"an":[25,70],"\u03b5-approximation":[26],"particular":[29],"takes":[34,96],"prohibitive":[36],"amount":[37],"time":[39],"space.":[41],"To":[42],"alleviate":[43],"some":[44],"this":[46,97,330,357,386],"cost,":[47],"we":[48,209,230,303],"introduce":[49],"two":[50,334],"new":[51,233,331,346,358,387,403,445,450],"algorithms":[52,152,234],"into":[53],"the":[54,78,87,113,133,144,159,164,174,196,237,242,249,255,271,280,283,365,372,396,412,424,434],"osprey":[55,353],"suite":[56],"protein":[58,214,221,250,262,440],"design:":[59],"fries,":[60],"Fast":[62],"Removal":[63],"Inadequately":[65],"Energied":[66],"Sequences,":[67],"EWAK*,":[69],"Energy":[71],"Window":[72],"Approximation":[73],"K*.":[75],"fries":[76],"pre-processes":[77],"sequence":[79,92,99,135,161],"space":[80,100,136,162],"limit":[82],"design":[84,134,222,308,425,441],"only":[86,173],"most":[88,122,175],"stable,":[89],"energetically":[90,176],"favorable":[91],"possibilities.":[93],"EWAK*":[94],"then":[95],"pruned":[98],"as":[101,225],"input":[102,160],"and,":[103],"using":[104,112,298,377],"energy":[107,115],"window,":[108],"calculates":[109],"scores":[111],"lowest":[114],"conformations.":[116,148],"We":[117,328,370],"expect":[118],"fries/EWAK*":[119,267,305,351],"be":[121],"useful":[123],"in":[124,132,167,264,279,322,352],"cases":[125],"where":[126],"there":[127],"are":[128,140],"many":[129],"unstable":[130],"sequences":[131],"when":[138],"users":[139],"satisfied":[141],"with":[142,333,400],"enumerating":[143],"low-energy":[145],"ensemble":[146],"In":[149],"combination,":[150],"these":[151,232,287],"retain":[154],"calculational":[155],"while":[157,181,202],"limiting":[158],"conformations":[165],"included":[166],"each":[168],"function":[170],"calculation":[171],"favorable,":[177],"effectively":[178],"reducing":[179],"runtime":[180],"still":[182],"enriching":[183],"desirable":[185],"sequences.":[186],"This":[187,402,430],"combined":[188,329],"approach":[189],"led":[190],"significant":[192],"speed-ups":[193],"compared":[194],"previous":[197,366,413],"state-of-the-art":[198],"multi-sequence":[199],"algorithm,":[200],"BBK*,":[201],"maintaining":[203],"its":[204,323],"efficiency":[205],"accuracy,":[207],"which":[208],"show":[210],"across":[211],"40":[212],"different":[213,275],"systems":[215],"total":[218],"2,826":[220],"problems.":[223],"Additionally,":[224],"proof":[227],"concept,":[229],"used":[231,304],"redesign":[236],"protein-protein":[238],"interface":[239],"(PPI)":[240],"c-Raf-RBD:KRas":[243,284],"complex.":[244,285],"Ras-binding":[246],"domain":[247],"kinase":[251],"c-Raf":[252],"(c-Raf-RBD)":[253],"is":[254],"tightest":[256],"known":[257,415],"binder":[258,416],"KRas,":[260],"implicated":[263],"difficult-to-treat":[265],"cancers.":[266],"accurately":[268],"retrospectively":[269],"predicted":[270,297,355],"effect":[272,292],"41":[274],"sets":[276],"mutations":[278,288,290,337],"PPI":[281],"Notably,":[286],"include":[289],"whose":[291],"had":[293],"previously":[294,335],"been":[295],"incorrectly":[296],"other":[299],"computational":[300,397,439],"methods.":[301],"Next,":[302],"prospective":[307,451],"discovered":[310],"novel":[312],"point":[313,427],"mutation":[314,332],"that":[315,356,385],"improves":[316],"binding":[317,373],"c-Raf-RBD":[319],"KRas":[321],"active,":[324],"GTP-bound":[325],"state":[326],"(KRasGTP).":[327],"reported":[336],"(which":[338],"were":[339],"highly-ranked":[340],"by":[341,442],"osprey)":[342],"create":[344],"variant":[347,359,388,404],"c-Raf-RBD,":[349],"c-Raf-RBD(RKY).":[350],"computationally":[354],"binds":[360,405],"even":[361],"more":[362,409,421],"tightly":[363,410,422],"than":[364,411,423],"best-binding":[367],"variant,":[368],"c-Raf-RBD(RK).":[369],"measured":[371],"affinity":[374,392],"c-Raf-RBD(RKY)":[376],"bio-layer":[379],"interferometry":[380],"(BLI)":[381],"assay,":[382],"found":[384],"exhibits":[389],"single-digit":[390],"nanomolar":[391],"KRasGTP,":[394],"confirming":[395],"predictions":[398],"made":[399],"fries/EWAK*.":[401],"roughly":[406,418],"five":[407],"times":[408,420],"best":[414],"36":[419],"starting":[426],"(wild-type":[428],"c-Raf-RBD).":[429],"study":[431],"steps":[432],"through":[433],"advancement":[435],"development":[437],"presenting":[443],"theory,":[444],"algorithms,":[446],"accurate":[447],"retrospective":[448],"designs,":[449,452],"biochemical":[454],"validation.":[455]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}