{"id":"https://openalex.org/W4377289860","doi":"https://doi.org/10.1371/journal.pcbi.1010680","title":"Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock","display_name":"Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock","publication_year":2023,"publication_date":"2023-05-22","ids":{"openalex":"https://openalex.org/W4377289860","doi":"https://doi.org/10.1371/journal.pcbi.1010680"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010680","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010680","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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1010680","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081264094","display_name":"William Sheffler","orcid":"https://orcid.org/0000-0002-3659-9559"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"William Sheffler","raw_affiliation_strings":["Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013293317","display_name":"Erin C. Yang","orcid":"https://orcid.org/0000-0002-1305-9066"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Erin C. Yang","raw_affiliation_strings":["Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, Washington, United States of America","Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","Department of Biochemistry, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074243944","display_name":"Quinton M. Dowling","orcid":"https://orcid.org/0000-0002-4634-0014"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Quinton Dowling","raw_affiliation_strings":["Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038577052","display_name":"Yang Hsia","orcid":"https://orcid.org/0000-0001-7467-8373"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yang Hsia","raw_affiliation_strings":["Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091502640","display_name":"Chelsea N. Fries","orcid":"https://orcid.org/0000-0002-2724-430X"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chelsea N. Fries","raw_affiliation_strings":["Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000212707","display_name":"Jenna Stanislaw","orcid":"https://orcid.org/0009-0002-5116-5318"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Jenna Stanislaw","raw_affiliation_strings":["Life and Medical Sciences Institute, University of Bonn, Bonn, Germany","Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","Transdisciplinary Research Area \"Building Blocks of Matter and Fundamental Interactions (TRA Matter)\", University of Bonn, Bonn, Germany","Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Life and Medical Sciences Institute, University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Transdisciplinary Research Area \"Building Blocks of Matter and Fundamental Interactions (TRA Matter)\", University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068143466","display_name":"Mark Langowski","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark D. Langowski","raw_affiliation_strings":["Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington, United States of America","Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074733235","display_name":"Marisa Brandys","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Marisa Brandys","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100356685","display_name":"Zhe Li","orcid":"https://orcid.org/0000-0002-9357-6839"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhe Li","raw_affiliation_strings":["Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087368548","display_name":"Rebecca Skotheim","orcid":"https://orcid.org/0009-0005-0757-8432"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rebecca Skotheim","raw_affiliation_strings":["Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038946848","display_name":"Andrew J. Borst","orcid":"https://orcid.org/0000-0003-4297-7824"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andrew J. Borst","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038302116","display_name":"Alena Khmelinskaia","orcid":"https://orcid.org/0000-0003-1584-9800"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["DE","US"],"is_corresponding":true,"raw_author_name":"Alena Khmelinskaia","raw_affiliation_strings":["Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","Transdisciplinary Research Area \"Building Blocks of Matter and Fundamental Interactions (TRA Matter)\", University of Bonn, Bonn, Germany","Life and Medical Sciences Institute, University of Bonn, Bonn, Germany","Department of Biochemistry, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Transdisciplinary Research Area \"Building Blocks of Matter and Fundamental Interactions (TRA Matter)\", University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"Life and Medical Sciences Institute, University of Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016851342","display_name":"Neil P. King","orcid":"https://orcid.org/0000-0002-2978-4692"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Neil P. King","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","Institute for Protein Design, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053192926","display_name":"David Baker","orcid":"https://orcid.org/0000-0001-7896-6217"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David Baker","raw_affiliation_strings":["Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America","Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","Department of Biochemistry, University of Washington, Seattle, Washington, United States of America"],"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I201448701"]},{"raw_affiliation_string":"Institute for Protein Design, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5000212707","https://openalex.org/A5013293317","https://openalex.org/A5016851342","https://openalex.org/A5038302116","https://openalex.org/A5038577052","https://openalex.org/A5038946848","https://openalex.org/A5053192926","https://openalex.org/A5068143466","https://openalex.org/A5074243944","https://openalex.org/A5074733235","https://openalex.org/A5081264094","https://openalex.org/A5087368548","https://openalex.org/A5091502640","https://openalex.org/A5100356685"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I135140700","https://openalex.org/I201448701"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2509,"currency":"EUR","value_usd":2705},"fwci":5.5553,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.96474906,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"19","issue":"5","first_page":"e1010680","last_page":"e1010680"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9975000023841858,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9975000023841858,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9952999949455261,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12505","display_name":"Peptidase Inhibition and Analysis","score":0.9927999973297119,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"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/docking","display_name":"Docking (animal)","score":0.7375568747520447},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5636686086654663},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5056562423706055},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.44836777448654175},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.43611425161361694},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.36972570419311523},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.31323015689849854},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2373640239238739},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1701691448688507},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13034561276435852},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.10760122537612915}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7375568747520447},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5636686086654663},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5056562423706055},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44836777448654175},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.43611425161361694},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.36972570419311523},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.31323015689849854},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2373640239238739},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1701691448688507},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13034561276435852},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.10760122537612915},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1010680","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010680","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":"pmh:oai:pubmedcentral.nih.gov:10237659","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10237659","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10237659/pdf/pcbi.1010680.pdf","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"},{"id":"pmh:oai:doaj.org/article:19afdf7c313d401a9ed335aa3e0d5a14","is_oa":true,"landing_page_url":"https://doaj.org/article/19afdf7c313d401a9ed335aa3e0d5a14","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 5, p e1010680 (2023)","raw_type":"article"},{"id":"pmh:oai:osti.gov:1974630","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1974630","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:osti.gov:1983380","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1983380","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:osti.gov:2420885","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2420885","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010680","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010680","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":[],"awards":[{"id":"https://openalex.org/G3459125281","display_name":null,"funder_award_id":"DE-SC0018940 MOD03","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4781801749","display_name":null,"funder_award_id":"P50AI150464","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5392361400","display_name":null,"funder_award_id":"INV-010680","funder_id":"https://openalex.org/F4320306137","funder_display_name":"Bill and Melinda Gates Foundation"},{"id":"https://openalex.org/G8871642182","display_name":null,"funder_award_id":"CHE-1629214","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320306137","display_name":"Bill and Melinda Gates Foundation","ror":"https://ror.org/0456r8d26"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1505986412","https://openalex.org/W1560197628","https://openalex.org/W1976603396","https://openalex.org/W2005109042","https://openalex.org/W2005763580","https://openalex.org/W2008708467","https://openalex.org/W2015526636","https://openalex.org/W2019691413","https://openalex.org/W2020964455","https://openalex.org/W2075987376","https://openalex.org/W2081821176","https://openalex.org/W2113495611","https://openalex.org/W2126103104","https://openalex.org/W2132184418","https://openalex.org/W2136675308","https://openalex.org/W2151460035","https://openalex.org/W2151581834","https://openalex.org/W2201713963","https://openalex.org/W2277678953","https://openalex.org/W2433987067","https://openalex.org/W2465190302","https://openalex.org/W2491008760","https://openalex.org/W2538859158","https://openalex.org/W2559856762","https://openalex.org/W2606439133","https://openalex.org/W2742537352","https://openalex.org/W2784051357","https://openalex.org/W2803604922","https://openalex.org/W2899747610","https://openalex.org/W2906649237","https://openalex.org/W2921646015","https://openalex.org/W2944245644","https://openalex.org/W2948101563","https://openalex.org/W2954867721","https://openalex.org/W2973382334","https://openalex.org/W3001044055","https://openalex.org/W3047128047","https://openalex.org/W3081283882","https://openalex.org/W3094860119","https://openalex.org/W3120712987","https://openalex.org/W3128196163","https://openalex.org/W3136996287","https://openalex.org/W3148609706","https://openalex.org/W3156929038","https://openalex.org/W3158342176","https://openalex.org/W4255594044","https://openalex.org/W4281626490","https://openalex.org/W4289874592","https://openalex.org/W4293676863","https://openalex.org/W4296031103","https://openalex.org/W4296032638","https://openalex.org/W4297236169","https://openalex.org/W4309504539","https://openalex.org/W4315487333","https://openalex.org/W4323535601","https://openalex.org/W6718104472","https://openalex.org/W6843565178","https://openalex.org/W6846625409","https://openalex.org/W6888865365"],"related_works":["https://openalex.org/W3187431608","https://openalex.org/W1974422922","https://openalex.org/W1988730649","https://openalex.org/W4309353019","https://openalex.org/W2095784700","https://openalex.org/W2170120749","https://openalex.org/W2067576503","https://openalex.org/W2199134476","https://openalex.org/W2170285690","https://openalex.org/W4372348062"],"abstract_inverted_index":{"Computationally":[0],"designed":[1],"multi-subunit":[2],"assemblies":[3,51],"have":[4],"shown":[5],"considerable":[6],"promise":[7],"for":[8,46,64,78,94,129],"a":[9,14,71,84,104,138],"variety":[10,139],"of":[11,17,21,33,57,87,123,140],"applications,":[12],"including":[13,137],"new":[15],"generation":[16],"potent":[18],"vaccines.":[19],"One":[20],"the":[22,121,124,134],"major":[23],"routes":[24],"to":[25,54,62,112,150],"such":[26,50],"materials":[27],"is":[28,91],"rigid":[29],"body":[30],"sequence-independent":[31,79],"docking":[32,47,82,117,154],"cyclic":[34],"oligomers":[35],"into":[36],"architectures":[37,89],"with":[38],"point":[39],"group":[40],"or":[41],"lattice":[42],"symmetries.":[43],"Current":[44],"methods":[45],"and":[48,59,74,103,132,143,152],"designing":[49],"are":[52,60],"tailored":[53],"specific":[55],"classes":[56],"symmetry":[58],"difficult":[61],"modify":[63],"novel":[65],"applications.":[66],"Here":[67],"we":[68],"describe":[69,120,133],"RPXDock,":[70],"fast,":[72],"flexible,":[73],"modular":[75],"software":[76],"package":[77],"rigid-body":[80],"protein":[81],"across":[83],"wide":[85],"range":[86],"symmetric":[88],"that":[90,146],"easily":[92],"customizable":[93],"further":[95],"development.":[96],"RPXDock":[97],"uses":[98],"an":[99],"efficient":[100],"hierarchical":[101],"search":[102,114],"residue-pair":[105],"transform":[106],"(":[107],"RPX":[108],")":[109],"scoring":[110],"method":[111],"rapidly":[113],"through":[115],"multidimensional":[116],"space.":[118],"We":[119],"structure":[122],"software,":[125],"provide":[126],"practical":[127],"guidelines":[128],"its":[130],"use,":[131],"available":[135],"functionalities":[136],"score":[141],"functions":[142],"filtering":[144],"tools":[145],"can":[147],"be":[148],"used":[149],"guide":[151],"refine":[153],"results":[155],"towards":[156],"desired":[157],"configurations.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":10}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2023-05-23T00:00:00"}
