{"id":"https://openalex.org/W2344557669","doi":"https://doi.org/10.1093/nar/gkw336","title":"3Drefine: an interactive web server for efficient protein structure refinement","display_name":"3Drefine: an interactive web server for efficient protein structure refinement","publication_year":2016,"publication_date":"2016-04-29","ids":{"openalex":"https://openalex.org/W2344557669","doi":"https://doi.org/10.1093/nar/gkw336","mag":"2344557669","pmid":"https://pubmed.ncbi.nlm.nih.gov/27131371"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkw336","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw336","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W406/7632825/gkw336.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/44/W1/W406/7632825/gkw336.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018409409","display_name":"Debswapna Bhattacharya","orcid":"https://orcid.org/0000-0002-9630-0141"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Debswapna Bhattacharya","raw_affiliation_strings":["Department of Computer Science, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024032800","display_name":"Jackson Nowotny","orcid":null},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jackson Nowotny","raw_affiliation_strings":["Department of Computer Science, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085487073","display_name":"Renzhi Cao","orcid":"https://orcid.org/0000-0002-8345-343X"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Renzhi Cao","raw_affiliation_strings":["Department of Computer Science, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044354277","display_name":"Jianlin Cheng","orcid":"https://orcid.org/0000-0003-0305-2853"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jianlin Cheng","raw_affiliation_strings":["Department of Computer Science, University of Missouri, Columbia, MO 65211, USA Informatics Institute, University of Missouri, Columbia, MO 65211, USA C. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA chengji@missouri.edu","Department of Computer Science, University of Missouri, Columbia, MO 65211, USA","Informatics Institute, University of Missouri, Columbia, MO 65211, USA","C. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Missouri, Columbia, MO 65211, USA Informatics Institute, University of Missouri, Columbia, MO 65211, USA C. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA chengji@missouri.edu","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Informatics Institute, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"C. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5044354277"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":15.493,"has_fulltext":false,"cited_by_count":439,"citation_normalized_percentile":{"value":0.99298512,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"44","issue":"W1","first_page":"W406","last_page":"W409"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9948999881744385,"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/computer-science","display_name":"Computer science","score":0.7334842681884766},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.7236822247505188},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5189670920372009},{"id":"https://openalex.org/keywords/protocol","display_name":"Protocol (science)","score":0.46641218662261963},{"id":"https://openalex.org/keywords/java-applet","display_name":"Java applet","score":0.45273345708847046},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.4507942795753479},{"id":"https://openalex.org/keywords/energy-minimization","display_name":"Energy minimization","score":0.43962588906288147},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.42882171273231506},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4243074059486389},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3935197591781616},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.3860645294189453},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.262516587972641},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.2032313048839569},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1485791802406311}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7334842681884766},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.7236822247505188},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5189670920372009},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.46641218662261963},{"id":"https://openalex.org/C15524039","wikidata":"https://www.wikidata.org/wiki/Q865817","display_name":"Java applet","level":3,"score":0.45273345708847046},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.4507942795753479},{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.43962588906288147},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.42882171273231506},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4243074059486389},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3935197591781616},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.3860645294189453},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.262516587972641},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.2032313048839569},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1485791802406311},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","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":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020169","descriptor_name":"Caspases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020169","descriptor_name":"Caspases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020169","descriptor_name":"Caspases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020169","descriptor_name":"Caspases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkw336","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw336","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W406/7632825/gkw336.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:27131371","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27131371","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:3952881","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4987902","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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:open-archive.highwire.org:nar:44/W1/W406","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/44/W1/W406","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/nar/gkw336","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkw336","pdf_url":"https://academic.oup.com/nar/article-pdf/44/W1/W406/7632825/gkw336.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.6299999952316284}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1968543088","https://openalex.org/W1998917415","https://openalex.org/W2008708467","https://openalex.org/W2011703027","https://openalex.org/W2051434435","https://openalex.org/W2052328791","https://openalex.org/W2071545816","https://openalex.org/W2080207615","https://openalex.org/W2099667027","https://openalex.org/W2101569554","https://openalex.org/W2110483430","https://openalex.org/W2117451312","https://openalex.org/W2122429432","https://openalex.org/W2129414710","https://openalex.org/W2136567909","https://openalex.org/W2142319132","https://openalex.org/W2150705899","https://openalex.org/W2154714625","https://openalex.org/W2158562723","https://openalex.org/W2161151688","https://openalex.org/W2165157960","https://openalex.org/W2333603558","https://openalex.org/W6702862858"],"related_works":["https://openalex.org/W2351253912","https://openalex.org/W2390343738","https://openalex.org/W2159711605","https://openalex.org/W2015864859","https://openalex.org/W3030051407","https://openalex.org/W2388298668","https://openalex.org/W2378101787","https://openalex.org/W191813162","https://openalex.org/W2007095478","https://openalex.org/W2612615462"],"abstract_inverted_index":{"3Drefine":[0,25,93,172,186],"is":[1,115,148],"an":[2],"interactive":[3,137],"web":[4,94,157,173,187],"server":[5,95,123,158,174,188],"for":[6,52,97],"consistent":[7,78],"and":[8,21,48,72,76,87,114,133,136,163],"computationally":[9],"efficient":[10,53],"protein":[11,54,99,152],"structure":[12,55,83,100],"refinement":[13,26,101],"with":[14,36,150],"the":[15,41,81,144,171,183,195],"capability":[16],"to":[17,182],"perform":[18],"web-based":[19],"statistical":[20,134],"visual":[22],"analysis.":[23],"The":[24,57,92,122,156,185],"protocol":[27],"utilizes":[28],"iterative":[29],"optimization":[30],"of":[31,128,139],"hydrogen":[32],"bonding":[33],"network":[34],"combined":[35],"atomic-level":[37],"energy":[38,132],"minimization":[39],"on":[40,63,70],"optimized":[42],"model":[43,153],"using":[44],"a":[45,103,169,177],"composite":[46],"physics":[47],"knowledge-based":[49],"force":[50],"fields":[51],"refinement.":[56],"method":[58],"has":[59,159,189],"been":[60,160,190],"extensively":[61,161],"evaluated":[62],"blind":[64],"CASP":[65],"experiments":[66],"as":[67,69],"well":[68],"large-scale":[71],"diverse":[73],"benchmark":[74],"datasets":[75],"exhibits":[77],"improvement":[79],"over":[80],"initial":[82],"in":[84],"both":[85],"global":[86],"local":[88],"structural":[89],"quality":[90],"measures.":[91],"allows":[96],"convenient":[98],"through":[102,130,143],"text":[104],"or":[105],"file":[106],"input":[107],"submission,":[108],"email":[109],"notification,":[110],"provided":[111],"example":[112],"submission":[113],"freely":[116],"available":[117,193],"without":[118],"any":[119],"registration":[120],"requirement.":[121],"also":[124],"provides":[125,176],"comprehensive":[126],"analysis":[127,154],"submissions":[129],"various":[131],"feedback":[135],"visualization":[138],"multiple":[140],"refined":[141],"models":[142],"JSmol":[145],"applet":[146],"that":[147],"equipped":[149],"numerous":[151],"tools.":[155],"tested":[162],"used":[164],"by":[165],"many":[166],"users.":[167],"As":[168],"result,":[170],"conveniently":[175],"useful":[178],"tool":[179],"easily":[180],"accessible":[181],"community.":[184],"made":[191],"publicly":[192],"at":[194],"URL:":[196],"http://sysbio.rnet.missouri.edu/3Drefine/.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":49},{"year":2023,"cited_by_count":54},{"year":2022,"cited_by_count":56},{"year":2021,"cited_by_count":100},{"year":2020,"cited_by_count":58},{"year":2019,"cited_by_count":41},{"year":2018,"cited_by_count":27},{"year":2017,"cited_by_count":19},{"year":2016,"cited_by_count":2}],"updated_date":"2026-05-21T09:19:25.381259","created_date":"2025-10-10T00:00:00"}
