{"id":"https://openalex.org/W2007804411","doi":"https://doi.org/10.1038/nmeth0809-551","title":"Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling","display_name":"Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling","publication_year":2009,"publication_date":"2009-07-30","ids":{"openalex":"https://openalex.org/W2007804411","doi":"https://doi.org/10.1038/nmeth0809-551","mag":"2007804411","pmid":"https://pubmed.ncbi.nlm.nih.gov/19644455","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2847683"},"language":"en","primary_location":{"id":"doi:10.1038/nmeth0809-551","doi":"https://doi.org/10.1038/nmeth0809-551","is_oa":false,"landing_page_url":"https://doi.org/10.1038/nmeth0809-551","pdf_url":null,"source":{"id":"https://openalex.org/S127827428","display_name":"Nature Methods","issn_l":"1548-7091","issn":["1548-7091","1548-7105"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Methods","raw_type":"journal-article"},"parent_works":[],"lineage":["https://openalex.org/W2007804411"],"child_works_count":0,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2847683/","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051399843","display_name":"Daniel J. Mandell","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel J Mandell","raw_affiliation_strings":["California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA","Graduate Program in Bioinformatics and Computational Biology,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I180670191"]},{"raw_affiliation_string":"Graduate Program in Bioinformatics and Computational Biology,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076012363","display_name":"Evangelos A. Coutsias","orcid":"https://orcid.org/0000-0003-2910-9125","observed_orcids":["https://orcid.org/0000-0003-2910-9125"]},"institutions":[{"id":"https://openalex.org/I169521973","display_name":"University of New Mexico","ror":"https://ror.org/05fs6jp91","country_code":"US","type":"education","lineage":["https://openalex.org/I169521973"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Evangelos A Coutsias","raw_affiliation_strings":["Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of New Mexico, Albuquerque, New Mexico, USA","institution_ids":["https://openalex.org/I169521973"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000906927","display_name":"Tanja Kortemme","orcid":"https://orcid.org/0000-0002-8494-680X","observed_orcids":["https://orcid.org/0000-0002-8494-680X"]},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tanja Kortemme","raw_affiliation_strings":["California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA","Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA","Graduate Program in Bioinformatics and Computational Biology,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California, USA","institution_ids":["https://openalex.org/I103922791","https://openalex.org/I180670191"]},{"raw_affiliation_string":"Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Graduate Program in Bioinformatics and Computational Biology,","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000906927"],"corresponding_institution_ids":["https://openalex.org/I103922791","https://openalex.org/I180670191"],"apc_list":{"value":12690,"currency":"USD","value_usd":12690},"apc_paid":null,"fwci":7.9372,"has_fulltext":false,"cited_by_count":462,"citation_normalized_percentile":{"value":0.98645446,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"6","issue":"8","first_page":"551","last_page":"552"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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":0.0003000000142492354,"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":9.999999747378752e-05,"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/conformational-sampling","display_name":"conformational sampling","score":0.890999972820282},{"id":"https://openalex.org/keywords/protein-structure-determination","display_name":"protein structure determination","score":0.7570000290870667},{"id":"https://openalex.org/keywords/integrative-modeling","display_name":"integrative modeling","score":0.4440000057220459},{"id":"https://openalex.org/keywords/protein-conformational-dynamics","display_name":"protein conformational dynamics","score":0.5210000276565552}],"concepts":[{"id":"https://openalex.org/C37407028","wikidata":"https://www.wikidata.org/wiki/Q81454","display_name":"Angstrom","level":2,"score":0.7842088341712952},{"id":"https://openalex.org/C34413123","wikidata":"https://www.wikidata.org/wiki/Q170978","display_name":"Robotics","level":3,"score":0.6779241561889648},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.5979288816452026},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5805935859680176},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.5097333788871765},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34947097301483154},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.33800071477890015},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.3214799761772156},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.29446038603782654},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2634487748146057},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.2539629340171814},{"id":"https://openalex.org/C90509273","wikidata":"https://www.wikidata.org/wiki/Q11012","display_name":"Robot","level":2,"score":0.18010610342025757},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1525437831878662},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09416323900222778},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1038/nmeth0809-551","doi":"https://doi.org/10.1038/nmeth0809-551","is_oa":false,"landing_page_url":"https://doi.org/10.1038/nmeth0809-551","pdf_url":null,"source":{"id":"https://openalex.org/S127827428","display_name":"Nature Methods","issn_l":"1548-7091","issn":["1548-7091","1548-7105"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Methods","raw_type":"journal-article"},{"id":"pmid:19644455","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19644455","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":"Nature methods","raw_type":"Letter"},{"id":"pmh:oai:pubmedcentral.nih.gov:2847683","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2847683/","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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Nat Methods","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.545.5593","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.545.5593","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.math.unm.edu/~vageli/papers/merged_manuscript.pdf","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:2847683","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC2847683/","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":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Nat Methods","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3926907971","display_name":null,"funder_award_id":"R01-GM08171","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4465623258","display_name":"Physics-Based Refinement of Comparative Protein Models","funder_award_id":"R01GM081710","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7036831238","display_name":"Center for Protein Folding Machinery","funder_award_id":"PN2EY016525","funder_id":"https://openalex.org/F4320337350","funder_display_name":"National Eye Institute"}],"funders":[{"id":"https://openalex.org/F4320337350","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":9,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1972026510","https://openalex.org/W1987660955","https://openalex.org/W1996443253","https://openalex.org/W2000443388","https://openalex.org/W2019476648","https://openalex.org/W2067484689","https://openalex.org/W2147752484","https://openalex.org/W2167612644"],"related_works":["https://openalex.org/W2972378442","https://openalex.org/W3195180621","https://openalex.org/W2040138931","https://openalex.org/W185409148","https://openalex.org/W2970543766","https://openalex.org/W1970858396","https://openalex.org/W4229822293","https://openalex.org/W2611842177","https://openalex.org/W2036499039"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":24},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":28},{"year":2022,"cited_by_count":31},{"year":2021,"cited_by_count":31},{"year":2020,"cited_by_count":31},{"year":2019,"cited_by_count":22},{"year":2018,"cited_by_count":39},{"year":2017,"cited_by_count":32},{"year":2016,"cited_by_count":41},{"year":2015,"cited_by_count":23},{"year":2014,"cited_by_count":19},{"year":2013,"cited_by_count":37},{"year":2012,"cited_by_count":32}],"updated_date":"2026-11-14T11:04:58.165337","created_date":"2016-06-24T00:00:00"}