{"id":"https://openalex.org/W1966111577","doi":"https://doi.org/10.1371/journal.pcbi.1000428","title":"Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations","display_name":"Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations","publication_year":2009,"publication_date":"2009-07-09","ids":{"openalex":"https://openalex.org/W1966111577","doi":"https://doi.org/10.1371/journal.pcbi.1000428","mag":"1966111577","pmid":"https://pubmed.ncbi.nlm.nih.gov/19593364"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000428","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000428","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000428&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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000428&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055130435","display_name":"Lucy R. Allen","orcid":null},"institutions":[{"id":"https://openalex.org/I130828816","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33","country_code":"GB","type":"education","lineage":["https://openalex.org/I130828816"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Lucy R. Allen","raw_affiliation_strings":["School of Physics & Astronomy, University of Leeds, Leeds, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Physics & Astronomy, University of Leeds, Leeds, United Kingdom","institution_ids":["https://openalex.org/I130828816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045646702","display_name":"Sergei V. Krivov","orcid":"https://orcid.org/0000-0002-3493-0068"},"institutions":[{"id":"https://openalex.org/I130828816","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33","country_code":"GB","type":"education","lineage":["https://openalex.org/I130828816"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Sergei V. Krivov","raw_affiliation_strings":["Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom","institution_ids":["https://openalex.org/I130828816"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025815526","display_name":"Emanuele Paci","orcid":"https://orcid.org/0000-0002-4891-2768"},"institutions":[{"id":"https://openalex.org/I130828816","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33","country_code":"GB","type":"education","lineage":["https://openalex.org/I130828816"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Emanuele Paci","raw_affiliation_strings":["Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom","School of Physics & Astronomy, University of Leeds, Leeds, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Institute of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom","institution_ids":["https://openalex.org/I130828816"]},{"raw_affiliation_string":"School of Physics & Astronomy, University of Leeds, Leeds, United Kingdom","institution_ids":["https://openalex.org/I130828816"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5025815526","https://openalex.org/A5045646702"],"corresponding_institution_ids":["https://openalex.org/I130828816"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.348,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.78971606,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"5","issue":"7","first_page":"e1000428","last_page":"e1000428"},"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":0.9957000017166138,"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":0.9944000244140625,"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/protein-folding","display_name":"Protein folding","score":0.6748583316802979},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5789185762405396},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.5278477668762207},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5136515498161316},{"id":"https://openalex.org/keywords/lattice-protein","display_name":"Lattice protein","score":0.5063618421554565},{"id":"https://openalex.org/keywords/energy-landscape","display_name":"Energy landscape","score":0.48953232169151306},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.47753989696502686},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4673771262168884},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.4361937344074249},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.43362659215927124},{"id":"https://openalex.org/keywords/downhill-folding","display_name":"Downhill folding","score":0.413490355014801},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.40901678800582886},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.39804330468177795},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.39637482166290283},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.38868239521980286},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.37338125705718994},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.281490296125412},{"id":"https://openalex.org/keywords/phi-value-analysis","display_name":"Phi value analysis","score":0.18814444541931152},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1439996063709259},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.12494039535522461},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.07697126269340515}],"concepts":[{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.6748583316802979},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5789185762405396},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.5278477668762207},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5136515498161316},{"id":"https://openalex.org/C32598905","wikidata":"https://www.wikidata.org/wiki/Q6497130","display_name":"Lattice protein","level":3,"score":0.5063618421554565},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.48953232169151306},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.47753989696502686},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4673771262168884},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.4361937344074249},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.43362659215927124},{"id":"https://openalex.org/C46449900","wikidata":"https://www.wikidata.org/wiki/Q5303170","display_name":"Downhill folding","level":4,"score":0.413490355014801},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.40901678800582886},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.39804330468177795},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.39637482166290283},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38868239521980286},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.37338125705718994},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.281490296125412},{"id":"https://openalex.org/C162203774","wikidata":"https://www.wikidata.org/wiki/Q7181581","display_name":"Phi value analysis","level":3,"score":0.18814444541931152},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1439996063709259},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.12494039535522461},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.07697126269340515},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D008958","descriptor_name":"Models, Molecular","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":"D008958","descriptor_name":"Models, Molecular","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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1371/journal.pcbi.1000428","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000428","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000428&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:19593364","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19593364","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:CiteSeerX.psu:10.1.1.794.4073","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.794.4073","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/b2/ae/pcbi.1000428.PMC2700257.pdf","raw_type":"text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1000428","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000428","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:cris.unibo.it:11585/885382","is_oa":false,"landing_page_url":"http://hdl.handle.net/11585/885382","pdf_url":null,"source":{"id":"https://openalex.org/S4306402579","display_name":"Archivio istituzionale della ricerca (Alma Mater Studiorum Universit\u00e0 di Bologna)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210117483","host_organization_name":"Istituto di Ematologia di Bologna","host_organization_lineage":["https://openalex.org/I4210117483"],"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":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:52538d2d89aa491aaa69a375a1d407ef","is_oa":true,"landing_page_url":"https://doaj.org/article/52538d2d89aa491aaa69a375a1d407ef","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-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 5, Iss 7, p e1000428 (2009)","raw_type":"article"},{"id":"pmh:oai:eprints.whiterose.ac.uk:10092","is_oa":true,"landing_page_url":"http://eprints.whiterose.ac.uk/10092/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400854","display_name":"White Rose Research Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"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":"Article"},{"id":"pmh:oai:figshare.com:article/147042","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Analysis_of_the_Free_Energy_Surface_of_Proteins_from_Reversible_Folding_Simulations/147042","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:2700257","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2700257","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1000428","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000428","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000428&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":[{"display_name":"Affordable and clean energy","score":0.7799999713897705,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1966111577.pdf","grobid_xml":"https://content.openalex.org/works/W1966111577.grobid-xml"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W1710827023","https://openalex.org/W1963871440","https://openalex.org/W1966743338","https://openalex.org/W1970440715","https://openalex.org/W1972675000","https://openalex.org/W1973667581","https://openalex.org/W1989817970","https://openalex.org/W1994787908","https://openalex.org/W2006460346","https://openalex.org/W2008708467","https://openalex.org/W2010160084","https://openalex.org/W2012616517","https://openalex.org/W2014460723","https://openalex.org/W2016367231","https://openalex.org/W2017546280","https://openalex.org/W2017776794","https://openalex.org/W2022239151","https://openalex.org/W2028660585","https://openalex.org/W2038494121","https://openalex.org/W2039592270","https://openalex.org/W2042423854","https://openalex.org/W2046241839","https://openalex.org/W2046799939","https://openalex.org/W2049043767","https://openalex.org/W2051116535","https://openalex.org/W2052124922","https://openalex.org/W2056559191","https://openalex.org/W2056975402","https://openalex.org/W2062759724","https://openalex.org/W2065065181","https://openalex.org/W2065864578","https://openalex.org/W2066041565","https://openalex.org/W2066952483","https://openalex.org/W2067798279","https://openalex.org/W2068450894","https://openalex.org/W2069479024","https://openalex.org/W2072290134","https://openalex.org/W2075845680","https://openalex.org/W2077412035","https://openalex.org/W2077555515","https://openalex.org/W2079094352","https://openalex.org/W2080656389","https://openalex.org/W2082759836","https://openalex.org/W2084642783","https://openalex.org/W2094993087","https://openalex.org/W2096125044","https://openalex.org/W2096599403","https://openalex.org/W2098093830","https://openalex.org/W2107696550","https://openalex.org/W2112154906","https://openalex.org/W2113701866","https://openalex.org/W2115005877","https://openalex.org/W2117516104","https://openalex.org/W2121479624","https://openalex.org/W2128954946","https://openalex.org/W2132262459","https://openalex.org/W2139327615","https://openalex.org/W2141509162","https://openalex.org/W2145326890","https://openalex.org/W2148634928","https://openalex.org/W2153415105","https://openalex.org/W2161504850","https://openalex.org/W2170860665","https://openalex.org/W2188961801","https://openalex.org/W6680088764"],"related_works":["https://openalex.org/W1994742030","https://openalex.org/W2476476683","https://openalex.org/W1974862140","https://openalex.org/W2057022167","https://openalex.org/W2097163770","https://openalex.org/W2049509393","https://openalex.org/W1982122959","https://openalex.org/W1990644981","https://openalex.org/W1988606236","https://openalex.org/W3022832097"],"abstract_inverted_index":{"Computer":[0],"generated":[1],"trajectories":[2,36,96],"can,":[3],"in":[4,67,97,104],"principle,":[5],"reveal":[6],"the":[7,25,76,88,114,119,125,149,165,188],"folding":[8,35,90],"pathways":[9],"of":[10,28,60,87,113,124,142,153,164,180,191],"a":[11,29,48,57,69,85,130,133,139,175],"protein":[12,93,126],"at":[13],"atomic":[14],"resolution":[15],"and":[16,20,64,79,100,106,121,170,173,177],"possibly":[17],"suggest":[18],"general":[19],"simple":[21,176],"rules":[22],"for":[23,47,56],"predicting":[24],"folded":[26,71],"structure":[27,72],"given":[30],"sequence.":[31],"While":[32],"such":[33,129,154],"reversible":[34],"can":[37,53],"only":[38],"be":[39,54],"determined":[40,55],"ab":[41],"initio":[42],"using":[43,62],"all-atom":[44],"transferable":[45],"force-fields":[46],"few":[49],"small":[50,140],"proteins,":[51],"they":[52],"large":[58],"number":[59,141],"proteins":[61],"coarse-grained":[63],"structure-based":[65],"force-fields,":[66],"which":[68,98,117],"known":[70],"is":[73],"by":[74],"construction":[75],"absolute":[77],"energy":[78],"free-energy":[80,115,166],"minimum.":[81],"Here":[82],"we":[83],"use":[84],"model":[86],"fast":[89],"helical":[91],"lambda-repressor":[92],"to":[94],"generate":[95],"native":[99],"non-native":[101],"states":[102],"are":[103,108],"equilibrium":[105],"transitions":[107],"accurately":[109],"sampled.":[110],"Yet,":[111],"representation":[112,163],"surface,":[116],"underlies":[118],"thermodynamic":[120],"dynamic":[122],"properties":[123],"model,":[127],"from":[128],"trajectory":[131],"remains":[132],"challenge.":[134],"Projections":[135],"over":[136],"one":[137],"or":[138],"arbitrarily":[143],"chosen":[144],"progress":[145],"variables":[146],"often":[147],"hide":[148],"most":[150],"important":[151,169],"features":[152],"surfaces.":[155],"The":[156],"results":[157],"unequivocally":[158],"show":[159],"that":[160],"an":[161],"unprojected":[162],"surface":[167],"provides":[168],"unbiased":[171],"information":[172],"allows":[174],"meaningful":[178],"description":[179],"many-dimensional,":[181],"heterogeneous":[182],"trajectories,":[183],"providing":[184],"new":[185],"insight":[186],"into":[187],"possible":[189],"mechanisms":[190],"fast-folding":[192],"proteins.":[193]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
