{"id":"https://openalex.org/W2166660130","doi":"https://doi.org/10.1371/journal.pcbi.1004368","title":"Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments","display_name":"Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments","publication_year":2015,"publication_date":"2015-10-27","ids":{"openalex":"https://openalex.org/W2166660130","doi":"https://doi.org/10.1371/journal.pcbi.1004368","mag":"2166660130","pmid":"https://pubmed.ncbi.nlm.nih.gov/26505197"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004368","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004368","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004368&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004368&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046743297","display_name":"Rong Shen","orcid":"https://orcid.org/0000-0003-4332-4518"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rong Shen","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117823207","display_name":"Wei Han","orcid":"https://orcid.org/0000-0003-0759-1766"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wei Han","raw_affiliation_strings":["Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","Beckman Institute, University of Illinois at Urbana\u2013Champaign, Urbana, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Beckman Institute, University of Illinois at Urbana\u2013Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041624726","display_name":"Giacomo Fiorin","orcid":"https://orcid.org/0000-0002-8793-8645"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Giacomo Fiorin","raw_affiliation_strings":["Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023497447","display_name":"Shahidul M. Islam","orcid":"https://orcid.org/0000-0001-5769-6844"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shahidul M. Islam","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029996336","display_name":"Klaus Schulten","orcid":"https://orcid.org/0000-0001-7192-9632"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Klaus Schulten","raw_affiliation_strings":["Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","Beckman Institute, University of Illinois at Urbana\u2013Champaign, Urbana, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]},{"raw_affiliation_string":"Beckman Institute, University of Illinois at Urbana\u2013Champaign, Urbana, Illinois, United States of America","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102778212","display_name":"Beno\u0131\u0302t Roux","orcid":"https://orcid.org/0000-0002-5254-2712"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Beno\u00eet Roux","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5023497447","https://openalex.org/A5029996336","https://openalex.org/A5041624726","https://openalex.org/A5046743297","https://openalex.org/A5102778212","https://openalex.org/A5117823207"],"corresponding_institution_ids":["https://openalex.org/I157725225","https://openalex.org/I40347166","https://openalex.org/I84392919"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.2701,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.92008589,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"11","issue":"10","first_page":"e1004368","last_page":"e1004368"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12381","display_name":"Electron Spin Resonance Studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12381","display_name":"Electron Spin Resonance Studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9986000061035156,"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/T10493","display_name":"Ion channel regulation and function","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"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7158061265945435},{"id":"https://openalex.org/keywords/molecular-model","display_name":"Molecular model","score":0.5083567500114441},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.5032767653465271},{"id":"https://openalex.org/keywords/steric-effects","display_name":"Steric effects","score":0.4700911045074463},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4630140960216522},{"id":"https://openalex.org/keywords/resolution","display_name":"Resolution (logic)","score":0.4497251510620117},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4463358521461487},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42482277750968933},{"id":"https://openalex.org/keywords/structural-biology","display_name":"Structural biology","score":0.41924434900283813},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4151556193828583},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4116235375404358},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3483307361602783},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.24642300605773926},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15768226981163025},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15161922574043274},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.10968351364135742},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09456348419189453}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7158061265945435},{"id":"https://openalex.org/C178910836","wikidata":"https://www.wikidata.org/wiki/Q2196961","display_name":"Molecular model","level":2,"score":0.5083567500114441},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5032767653465271},{"id":"https://openalex.org/C201194858","wikidata":"https://www.wikidata.org/wiki/Q898238","display_name":"Steric effects","level":2,"score":0.4700911045074463},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4630140960216522},{"id":"https://openalex.org/C138268822","wikidata":"https://www.wikidata.org/wiki/Q1051925","display_name":"Resolution (logic)","level":2,"score":0.4497251510620117},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4463358521461487},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42482277750968933},{"id":"https://openalex.org/C191120209","wikidata":"https://www.wikidata.org/wiki/Q908902","display_name":"Structural biology","level":2,"score":0.41924434900283813},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4151556193828583},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4116235375404358},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3483307361602783},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.24642300605773926},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15768226981163025},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15161922574043274},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.10968351364135742},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09456348419189453},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D026901","descriptor_name":"Membrane Transport Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":11,"locations":[{"id":"doi:10.1371/journal.pcbi.1004368","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004368","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004368&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:26505197","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26505197","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:uchicago.tind.io:7496","is_oa":true,"landing_page_url":"http://knowledge.uchicago.edu/record/7496","pdf_url":null,"source":{"id":"https://openalex.org/S4306402460","display_name":"Knowledge@UChicago (University of Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40347166","host_organization_name":"University of Chicago","host_organization_lineage":["https://openalex.org/I40347166"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://knowledge.uchicago.edu/record/7496","raw_type":"Text"},{"id":"pmh:doi:10.6082/1a215-8y855","is_oa":true,"landing_page_url":"https://knowledge.uchicago.edu/communities/biological-sciences-division/","pdf_url":null,"source":{"id":"https://openalex.org/S4406922384","display_name":"Open MIND","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},{"id":"pmh:oai:RePEc:plo:pcbi00:1004368","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004368","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:c061c6216e254f7fb7e8a2eab69e9d92","is_oa":true,"landing_page_url":"https://doaj.org/article/c061c6216e254f7fb7e8a2eab69e9d92","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,"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 11, Iss 10, p e1004368 (2015)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3610783","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4624691","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/1586671","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Structural_Refinement_of_Proteins_by_Restrained_Molecular_Dynamics_Simulations_with_Non_interacting_Molecular_Fragments_/1586671","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:4624691","is_oa":true,"landing_page_url":"http://doi.org/10.1371/journal.pcbi.1004368","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"doi:10.6082/1a215-8y855","is_oa":true,"landing_page_url":"https://doi.org/10.6082/1a215-8y855","pdf_url":null,"source":{"id":"https://openalex.org/S7407053018","display_name":"University of Chicago","issn_l":null,"issn":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.6082/4w0ar-fqk87","is_oa":true,"landing_page_url":"https://doi.org/10.6082/4w0ar-fqk87","pdf_url":null,"source":{"id":"https://openalex.org/S7407053018","display_name":"University of Chicago","issn_l":null,"issn":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004368","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004368","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004368&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1104241873","display_name":null,"funder_award_id":"P41 GM104601","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1191631772","display_name":null,"funder_award_id":"P41 RR005969","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G1212345030","display_name":null,"funder_award_id":"P41-RR005969","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1212448822","display_name":null,"funder_award_id":"P41-RR005969","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G3051408648","display_name":null,"funder_award_id":"S10 OD018495","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3110587493","display_name":null,"funder_award_id":"U54-GM087519","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3377026552","display_name":null,"funder_award_id":"RR005969","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4845568250","display_name":null,"funder_award_id":"R01-GM067887","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4953999220","display_name":null,"funder_award_id":"R01-GM067887","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5435107309","display_name":null,"funder_award_id":"1S10OD018495","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5545347726","display_name":null,"funder_award_id":"GM087519","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5921814723","display_name":null,"funder_award_id":"U54 GM087519","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7267382639","display_name":null,"funder_award_id":"R01 GM067887","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8465151711","display_name":null,"funder_award_id":"U54-GM087519","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309626","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"},{"id":"https://openalex.org/F4320338284","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2166660130.pdf","grobid_xml":"https://content.openalex.org/works/W2166660130.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W1539918506","https://openalex.org/W1602265064","https://openalex.org/W1643706501","https://openalex.org/W1800266928","https://openalex.org/W1969129798","https://openalex.org/W1970645504","https://openalex.org/W1972758026","https://openalex.org/W1973796039","https://openalex.org/W1974030600","https://openalex.org/W1975073708","https://openalex.org/W1975699701","https://openalex.org/W1976499671","https://openalex.org/W1979295135","https://openalex.org/W1983520523","https://openalex.org/W1989661323","https://openalex.org/W1999108741","https://openalex.org/W1999534297","https://openalex.org/W1999805574","https://openalex.org/W2000181571","https://openalex.org/W2003321601","https://openalex.org/W2015233467","https://openalex.org/W2017522634","https://openalex.org/W2020448043","https://openalex.org/W2023387861","https://openalex.org/W2027408247","https://openalex.org/W2029667189","https://openalex.org/W2033233860","https://openalex.org/W2033451549","https://openalex.org/W2035687084","https://openalex.org/W2038758364","https://openalex.org/W2042238972","https://openalex.org/W2049520220","https://openalex.org/W2054058473","https://openalex.org/W2062421111","https://openalex.org/W2064390126","https://openalex.org/W2065204180","https://openalex.org/W2067051406","https://openalex.org/W2068719415","https://openalex.org/W2072969174","https://openalex.org/W2073268852","https://openalex.org/W2073920564","https://openalex.org/W2077082977","https://openalex.org/W2080056514","https://openalex.org/W2084367350","https://openalex.org/W2098499866","https://openalex.org/W2101385347","https://openalex.org/W2104415321","https://openalex.org/W2106140689","https://openalex.org/W2109154308","https://openalex.org/W2120771179","https://openalex.org/W2133958173","https://openalex.org/W2143070723","https://openalex.org/W2144420181","https://openalex.org/W2144723737","https://openalex.org/W2150981663","https://openalex.org/W2151525286","https://openalex.org/W2154420373","https://openalex.org/W2157696981","https://openalex.org/W2164437435","https://openalex.org/W2164659462","https://openalex.org/W2164829352","https://openalex.org/W2314956016","https://openalex.org/W2315787811","https://openalex.org/W2327429313"],"related_works":["https://openalex.org/W2047041070","https://openalex.org/W1518653219","https://openalex.org/W2072172337","https://openalex.org/W3113041276","https://openalex.org/W4390487607","https://openalex.org/W4288061531","https://openalex.org/W1983338994","https://openalex.org/W2607853144","https://openalex.org/W179641246","https://openalex.org/W3126783617"],"abstract_inverted_index":{"The":[0,170,196,222,256],"knowledge":[1],"of":[2,13,20,60,68,87,173,175,215,219,230,235,268],"multiple":[3,113,149],"conformational":[4,29,70,217],"states":[5,30],"is":[6,35,103,144,179,184,203,224],"a":[7,124,136,212],"prerequisite":[8],"to":[9,64,89,106,122,146,191,206,210,253],"understand":[10],"the":[11,18,58,104,110,130,176,200,208,216,220,228,231,236,241,247,265,269,274],"function":[12],"membrane":[14],"transport":[15],"proteins.":[16],"Unfortunately,":[17],"determination":[19],"detailed":[21],"atomic":[22,168],"structures":[23,259],"for":[24],"all":[25,109,167,199],"these":[26,91],"functionally":[27],"important":[28,49,85],"with":[31,57,80,99,129,166,264],"conventional":[32],"high-resolution":[33],"approaches":[34,46],"often":[36],"difficult":[37],"and":[38,44,75,244,273],"unsuccessful.":[39],"In":[40,72],"some":[41],"cases,":[42],"biophysical":[43],"biochemical":[45],"can":[47,54],"provide":[48],"complementary":[50],"structural":[51,66,93,126,141],"information":[52,88,111,197],"that":[53],"be":[55],"exploited":[56,204],"help":[59],"advanced":[61],"computational":[62],"methods":[63],"derive":[65,123],"models":[67],"specific":[69],"states.":[71],"particular,":[73],"functional":[74],"spectroscopic":[76],"measurements":[77],"in":[78,240,261],"combination":[79],"site-directed":[81],"mutations":[82,118],"constitute":[83],"one":[84],"source":[86],"obtain":[90],"mixed-resolution":[92],"models.":[94],"A":[95],"very":[96],"common":[97],"problem":[98],"this":[100,134],"strategy,":[101],"however,":[102],"difficulty":[105],"simultaneously":[107,147,205],"integrate":[108],"from":[112,198,278],"independent":[114],"experiments":[115,280],"involving":[116],"different":[117,188],"or":[119,157],"chemical":[120],"labels":[121],"unique":[125],"model":[127,214,267],"consistent":[128],"data.":[131],"To":[132],"resolve":[133],"issue,":[135],"novel":[137],"restrained":[138],"molecular":[139,164,177,189,201],"dynamics":[140],"refinement":[142],"method":[143,223],"developed":[145],"incorporate":[148],"experimentally":[150],"determined":[151],"constraints":[152],"(e.g.,":[153],"engineered":[154],"metal":[155],"bridges":[156],"spin-labels),":[158],"each":[159,174],"treated":[160,180],"as":[161],"an":[162],"individual":[163],"fragment":[165],"details.":[169],"internal":[171],"structure":[172,229],"fragments":[178,190,202],"realistically,":[181],"while":[182],"there":[183],"no":[185],"interaction":[186],"between":[187,250],"avoid":[192],"unphysical":[193],"steric":[194],"clashes.":[195],"constrain":[207],"backbone":[209],"refine":[211],"three-dimensional":[213],"state":[218,243,271],"protein.":[221],"illustrated":[225],"by":[226,245],"refining":[227],"voltage-sensing":[232],"domain":[233],"(VSD)":[234],"Kv1.2":[237],"potassium":[238],"channel":[239],"resting":[242,270],"exploring":[246],"distance":[248,276],"histograms":[249,277],"spin-labels":[251],"attached":[252],"T4":[254,282],"lysozyme.":[255],"resulting":[257],"VSD":[258,272],"are":[260,284],"good":[262],"agreement":[263],"consensus":[266],"spin-spin":[275],"ESR/DEER":[279],"on":[281],"lysozyme":[283],"accurately":[285],"reproduced.":[286]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}