{"id":"https://openalex.org/W3040969795","doi":"https://doi.org/10.1371/journal.pcbi.1007970","title":"Real time structural search of the Protein Data Bank","display_name":"Real time structural search of the Protein Data Bank","publication_year":2020,"publication_date":"2020-07-08","ids":{"openalex":"https://openalex.org/W3040969795","doi":"https://doi.org/10.1371/journal.pcbi.1007970","mag":"3040969795","pmid":"https://pubmed.ncbi.nlm.nih.gov/32639954","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/7371193"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007970","doi":"https://doi.org/10.1371/journal.pcbi.1007970","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007970","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007970&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,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"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"},"volume":null,"type":"article","is_traditional":true,"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.1007970&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013018624","display_name":"Dmytro Guzenko","orcid":"https://orcid.org/0000-0002-8688-7460","observed_orcids":["https://orcid.org/0000-0002-8688-7460"]},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dmytro Guzenko","raw_affiliation_strings":["RCSB Protein Data Bank, San Diego Supercomputer Center University of California, San Diego, La Jolla, CA 92093, USA","RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068648875","display_name":"Stephen Kevin Burley","orcid":"https://orcid.org/0000-0002-2487-9713","observed_orcids":["https://orcid.org/0000-0002-2487-9713"]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4390039325","display_name":"Rutgers Cancer Institute","ror":"https://ror.org/0060x3y55","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I102322142","https://openalex.org/I4390039302","https://openalex.org/I4390039325"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen K. Burley","raw_affiliation_strings":["Cancer Institute of New Jersey, Rutgers The State University of New Jersey, New Brunswick, NJ 08903, USA","RCSB Protein Data Bank, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey, Piscataway, NJ08854, USA","RCSB Protein Data Bank, San Diego Supercomputer Center University of California, San Diego, La Jolla, CA 92093, USA","Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego, La Jolla, CA 92093, USA","Cancer Institute of New Jersey, Rutgers The State University of New Jersey, New Brunswick, New Jersey, United States of America","RCSB Protein Data Bank, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America","RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America","Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Institute of New Jersey, Rutgers The State University of New Jersey, New Brunswick, NJ 08903, USA","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I4390039325"]},{"raw_affiliation_string":"RCSB Protein Data Bank, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey, Piscataway, NJ08854, USA","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Cancer Institute of New Jersey, Rutgers The State University of New Jersey, New Brunswick, New Jersey, United States of America","institution_ids":["https://openalex.org/I102322142","https://openalex.org/I4390039325"]},{"raw_affiliation_string":"RCSB Protein Data Bank, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America","institution_ids":["https://openalex.org/I102322142"]},{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003460293","display_name":"Jos\u00e9 M. Duarte","orcid":"https://orcid.org/0000-0002-9544-5621","observed_orcids":["https://orcid.org/0000-0002-9544-5621","https://orcid.org/0000-0001-9220-3574"]},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jose M. Duarte","raw_affiliation_strings":["RCSB Protein Data Bank, San Diego Supercomputer Center University of California, San Diego, La Jolla, CA 92093, USA","RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center University of California, San Diego, La Jolla, CA 92093, USA","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"raw_affiliation_string":"RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5003460293"],"corresponding_institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959"],"apc_list":{"value":2500,"currency":"USD","value_usd":2500},"apc_paid":{"value":2500,"currency":"USD","value_usd":2500},"fwci":2.7635,"has_fulltext":true,"cited_by_count":62,"citation_normalized_percentile":{"value":0.92449036,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"16","issue":"7","first_page":"e1007970","last_page":"e1007970"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5282999873161316,"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":0.5282999873161316,"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/T11162","display_name":"Enzyme Structure and Function","score":0.4584999978542328,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T10211","display_name":"Computational Drug Discovery Methods","score":0.002400000113993883,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-structure-similarity","display_name":"protein structural similarity","score":0.8569999933242798},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"structural alignment","score":0.4749999940395355},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.8169999718666077},{"id":"https://openalex.org/keywords/shape-retrieval","display_name":"shape retrieval","score":0.5149999856948853}],"concepts":[{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.932687520980835},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.8962249159812927},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6135687828063965},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5742315649986267},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.5172563195228577},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5137990117073059},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.47352835536003113},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45519742369651794},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4419757127761841},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.4227929711341858},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3489236831665039},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27767932415008545},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23383688926696777},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.08008182048797607},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07938021421432495},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1007970","doi":"https://doi.org/10.1371/journal.pcbi.1007970","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007970","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007970&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,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"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":"doi:10.1101/845123","doi":"https://doi.org/10.1101/845123","is_oa":true,"landing_page_url":"https://doi.org/10.1101/845123","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/05/11/845123.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:7371193","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7371193","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmid:32639954","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32639954","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,"listed_in":[],"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":"Journal Article"},{"id":"pmh:oai:alma.01RUT_INST:11664907290004646","doi":null,"is_oa":false,"landing_page_url":"https://scholarship.libraries.rutgers.edu/esploro/outputs/journalArticle/Real-time-structural-search-of-the/991031665438304646","pdf_url":null,"source":{"id":"https://openalex.org/S4306401388","display_name":"Rutgers University Community Repository (Rutgers University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I102322142","host_organization_name":"Rutgers, The State University of New Jersey","host_organization_lineage":["https://openalex.org/I102322142"],"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":"text"},{"id":"pmh:oai:doaj.org/article:b567fa7776604fe1aa12e25bb981f82a","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/b567fa7776604fe1aa12e25bb981f82a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 7, p e1007970 (2020)","raw_type":"article"},{"id":"pmh:oai:osti.gov:1637743","doi":null,"is_oa":false,"landing_page_url":"https://www.osti.gov/biblio/1637743","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,"listed_in":[],"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:1639145","doi":null,"is_oa":false,"landing_page_url":"https://www.osti.gov/biblio/1639145","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,"listed_in":[],"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:1803884","doi":null,"is_oa":false,"landing_page_url":"https://www.osti.gov/biblio/1803884","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,"listed_in":[],"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.1007970","doi":"https://doi.org/10.1371/journal.pcbi.1007970","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007970","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007970&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,"listed_in":["anvur-scientific","ccf-b","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-140","russia-white-list-1","vabb-shw"],"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":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1378632953","display_name":"PDB Management by The Research Collaboratory for Structural Bioinformatics","funder_award_id":"1832184","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1558159524","display_name":null,"funder_award_id":"DBI-1832184","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1835487027","display_name":null,"funder_award_id":"DBI-1832184","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G187594386","display_name":null,"funder_award_id":"R01GM133198","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2688445917","display_name":"PDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS","funder_award_id":"R01GM133198","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G292810974","display_name":null,"funder_award_id":"DE-SC0019749","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7709312183","display_name":null,"funder_award_id":"R01GM133198","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8278765382","display_name":"PDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS","funder_award_id":"DESC0019749","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3040969795.pdf","grobid_xml":"https://content.openalex.org/works/W3040969795.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1503589039","https://openalex.org/W1535715635","https://openalex.org/W1565705317","https://openalex.org/W1911270099","https://openalex.org/W1965827393","https://openalex.org/W1972148314","https://openalex.org/W1998088403","https://openalex.org/W2000722212","https://openalex.org/W2005567617","https://openalex.org/W2022058405","https://openalex.org/W2046986600","https://openalex.org/W2050330741","https://openalex.org/W2051567790","https://openalex.org/W2057350662","https://openalex.org/W2077743314","https://openalex.org/W2081771568","https://openalex.org/W2085277871","https://openalex.org/W2091506983","https://openalex.org/W2094262711","https://openalex.org/W2102245393","https://openalex.org/W2112087820","https://openalex.org/W2113012330","https://openalex.org/W2114459720","https://openalex.org/W2116995042","https://openalex.org/W2119342149","https://openalex.org/W2123681603","https://openalex.org/W2125852558","https://openalex.org/W2136567909","https://openalex.org/W2137955461","https://openalex.org/W2141853020","https://openalex.org/W2144998676","https://openalex.org/W2152326664","https://openalex.org/W2160082320","https://openalex.org/W2558272290","https://openalex.org/W2600993444","https://openalex.org/W2751260413","https://openalex.org/W2898210859","https://openalex.org/W2898364362","https://openalex.org/W2913093503","https://openalex.org/W2947698700","https://openalex.org/W2950466381"],"related_works":["https://openalex.org/W2804271177","https://openalex.org/W2163016858","https://openalex.org/W42190837","https://openalex.org/W2531041418","https://openalex.org/W1949910768","https://openalex.org/W1911270099","https://openalex.org/W2033171295","https://openalex.org/W2070741080","https://openalex.org/W7099138371","https://openalex.org/W6930738688"],"abstract_inverted_index":{"Abstract":[0],"Detection":[1],"of":[2,26,42,72,97,133,186,197,251,262,307],"protein":[3,28,188,216,241],"structure":[4],"similarity":[5,121,239,274,356],"is":[6,32,100,174,205,210,268,286,343],"a":[7,27,76,101,108,137,233,292,302,349],"central":[8],"challenge":[9],"in":[10,45,183,190,271,301,314,339],"structural":[11],"bioinformatics.":[12],"Comparisons":[13],"are":[14,164],"usually":[15],"performed":[16],"at":[17,161,258],"the":[18,23,30,46,70,180,184,191,195,202,223,228,272,315,322],"polypeptide":[19,77,220],"chain":[20,78,281],"level,":[21],"however":[22],"functional":[24],"form":[25],"within":[29,75],"cell":[31],"often":[33],"an":[34],"oligomer.":[35],"This":[36,209],"fact,":[37],"together":[38,144],"with":[39,122,127,145,218,291],"recent":[40],"growth":[41,182],"oligomeric":[43,56],"structures":[44,154,189],"Protein":[47,153,192],"Data":[48,193],"Bank":[49],"(PDB),":[50],"demands":[51],"more":[52,269,351],"efficient":[53],"approaches":[54],"to":[55,114,176,200,288,327,330,361],"assembly":[57],"alignment/retrieval.":[58],"Traditional":[59],"methods":[60],"use":[61],"atom":[62],"level":[63],"information,":[64],"which":[65],"can":[66,84,237],"be":[67,85,289,325,328],"complicated":[68],"by":[69,87,167],"presence":[71],"topological":[73],"permutations":[74],"and/or":[79],"subunit":[80],"rearrangements.":[81],"These":[82],"challenges":[83],"overcome":[86],"comparing":[88,198],"electron":[89,116],"density":[90,117,263],"volumes":[91,118,261],"directly.":[92],"But,":[93],"brute":[94],"force":[95],"alignment":[96],"3D":[98,109,297],"data":[99],"compute":[102],"intensive":[103],"search":[104],"problem.":[105],"We":[106],"developed":[107],"Zernike":[110,298,308],"moment":[111],"normalization":[112,342],"procedure":[113],"orient":[115],"and":[119,170,243,280,345],"assess":[120],"unprecedented":[123],"speed.":[124],"Similarity":[125],"searching":[126],"this":[128,341],"approach":[129],"enables":[130],"real-time":[131],"retrieval":[132],"proteins/protein":[134],"assemblies":[135,217],"resembling":[136],"target,":[138],"from":[139,266],"PDB":[140],"or":[141,253],"user":[142],"input,":[143],"resulting":[146,300],"alignments":[147],"(":[148],"http://shape.rcsb.org":[149],").":[150],"Author":[151],"Summary":[152],"possess":[155],"wildly":[156],"varied":[157],"shapes,":[158,358],"but":[159],"patterns":[160,204],"different":[162],"levels":[163],"frequently":[165],"reused":[166],"nature.":[168],"Finding":[169],"classifying":[171],"these":[172],"similarities":[173],"fundamental":[175],"understand":[177],"evolution.":[178],"Given":[179],"continued":[181],"number":[185],"known":[187,295],"Bank,":[194],"task":[196],"them":[199],"find":[201],"common":[203],"becoming":[206],"increasingly":[207],"complicated.":[208],"especially":[211],"true":[212],"when":[213,317,359],"considering":[214],"complete":[215],"several":[219],"chains,":[221],"where":[222],"large":[224],"sizes":[225],"further":[226],"complicate":[227],"issue.":[229],"Here":[230,335],"we":[231,336],"present":[232],"novel":[234],"method":[235,256,353],"that":[236,244,321,338,346],"detect":[238],"between":[240,357],"shapes":[242],"works":[245],"equally":[246],"fast":[247],"for":[248,354],"any":[249],"size":[250],"proteins":[252,259],"assemblies.":[254],"The":[255,310],"looks":[257],"as":[260,296,305],"distribution,":[264],"departing":[265],"what":[267],"usual":[270],"field:":[273],"assessment":[275],"based":[276],"on":[277],"atomic":[278],"coordinates":[279],"connectivity.":[282],"A":[283],"volumetric":[284],"function":[285],"amenable":[287],"decomposed":[290],"mathematical":[293],"tool":[294,311],"polynomials,":[299],"compact":[303],"description":[304],"vectors":[306],"moments.":[309],"was":[312,319],"introduced":[313],"1990s,":[316],"it":[318,347],"suggested":[320],"moments":[323],"could":[324],"normalized":[326],"invariant":[329],"rotations":[331],"without":[332],"losing":[333],"information.":[334],"demonstrate":[337],"fact":[340],"possible":[344],"offers":[348],"much":[350],"accurate":[352],"assessing":[355],"compared":[360],"previous":[362],"attempts.":[363]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":3}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2020-07-16T00:00:00"}
