{"id":"https://openalex.org/W2008758209","doi":"https://doi.org/10.1021/ct500718s","title":"Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States","display_name":"Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States","publication_year":2014,"publication_date":"2014-12-12","ids":{"openalex":"https://openalex.org/W2008758209","doi":"https://doi.org/10.1021/ct500718s","mag":"2008758209","pmid":"https://pubmed.ncbi.nlm.nih.gov/26574197"},"language":"en","primary_location":{"id":"doi:10.1021/ct500718s","doi":"https://doi.org/10.1021/ct500718s","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ct500718s","pdf_url":null,"source":{"id":"https://openalex.org/S189701308","display_name":"Journal of Chemical Theory and Computation","issn_l":"1549-9618","issn":["1549-9618","1549-9626"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Theory and Computation","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://infoscience.epfl.ch/record/208426","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034005739","display_name":"Ferruccio Palazzesi","orcid":"https://orcid.org/0000-0003-1534-4781","observed_orcids":["https://orcid.org/0000-0003-1534-4781"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I57201433","display_name":"Universit\u00e0 della Svizzera italiana","ror":"https://ror.org/03c4atk17","country_code":"CH","type":"education","lineage":["https://openalex.org/I57201433"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Ferruccio Palazzesi","raw_affiliation_strings":["Department\rof Chemistry and Applied Biosciences, Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich, CH-8093 Zurich, Switzerland","Facolt\u00e1\rdi Informatica, Istituto di Scienze Computazionali, Universit\u00e1 della Svizzera Italiana, 6900 Lugano, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Chemistry and Applied Biosciences, Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich, CH-8093 Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Facolt\u00e1\rdi Informatica, Istituto di Scienze Computazionali, Universit\u00e1 della Svizzera Italiana, 6900 Lugano, Switzerland","institution_ids":["https://openalex.org/I57201433"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056999270","display_name":"Meher K. Prakash","orcid":"https://orcid.org/0000-0002-0091-4158","observed_orcids":["https://orcid.org/0000-0002-0091-4158"]},"institutions":[{"id":"https://openalex.org/I147481903","display_name":"Jawaharlal Nehru Centre for Advanced Scientific Research","ror":"https://ror.org/0538gdx71","country_code":"IN","type":"facility","lineage":["https://openalex.org/I147481903","https://openalex.org/I2799351866","https://openalex.org/I4210098748","https://openalex.org/I4210134808"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Meher K. Prakash","raw_affiliation_strings":["Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur, Bangalore, Karnataka, 500064, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur, Bangalore, Karnataka, 500064, India","institution_ids":["https://openalex.org/I147481903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056483461","display_name":"Massimiliano Bonomi","orcid":"https://orcid.org/0000-0002-7321-0004","observed_orcids":["https://orcid.org/0000-0002-7321-0004"]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Massimiliano Bonomi","raw_affiliation_strings":["Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044840019","display_name":"Alessandro Barducci","orcid":"https://orcid.org/0000-0002-1911-8039","observed_orcids":["https://orcid.org/0000-0002-1911-8039"]},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Alessandro Barducci","raw_affiliation_strings":["Laboratoire\rde Biophysique Statistique, \u00c8cole Polytechnique F\u00e8d\u00e8rale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire\rde Biophysique Statistique, \u00c8cole Polytechnique F\u00e8d\u00e8rale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5034005739","https://openalex.org/A5044840019"],"corresponding_institution_ids":["https://openalex.org/I35440088","https://openalex.org/I5124864","https://openalex.org/I57201433"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":5.1021,"has_fulltext":false,"cited_by_count":120,"citation_normalized_percentile":{"value":0.97019903,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":"11","issue":"1","first_page":"2","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"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":1.0,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.0,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-intrinsic-disorder","display_name":"protein disorder","score":0.699999988079071},{"id":"https://openalex.org/keywords/intrinsically-disordered-peptides","display_name":"intrinsically disordered peptides","score":0.8759999871253967},{"id":"https://openalex.org/keywords/all-atom-force-field","display_name":"all-atom force field","score":0.8519999980926514},{"id":"https://openalex.org/keywords/force-field-accuracy","display_name":"force field accuracy","score":0.8259999752044678},{"id":"https://openalex.org/keywords/enhanced-sampling","display_name":"enhanced sampling","score":0.7580000162124634},{"id":"https://openalex.org/keywords/conformational-ensembles","display_name":"conformational ensembles","score":0.7329999804496765}],"concepts":[{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.6844354271888733},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6684479713439941},{"id":"https://openalex.org/C148043351","wikidata":"https://www.wikidata.org/wiki/Q4456944","display_name":"Current (fluid)","level":2,"score":0.572256863117218},{"id":"https://openalex.org/C2778815515","wikidata":"https://www.wikidata.org/wiki/Q3408242","display_name":"Intrinsically disordered proteins","level":2,"score":0.5192723274230957},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.4674108326435089},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.4406890273094177},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.4383273124694824},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.41611248254776},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3746235966682434},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.33914822340011597},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32549208402633667},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.30497559905052185},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.27414315938949585},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.2712255120277405},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.13813626766204834},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.12046325206756592},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.08296370506286621},{"id":"https://openalex.org/C94915269","wikidata":"https://www.wikidata.org/wiki/Q1834857","display_name":"Detector","level":2,"score":0.0},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019906","descriptor_name":"Nuclear Magnetic Resonance, Biomolecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/ct500718s","doi":"https://doi.org/10.1021/ct500718s","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ct500718s","pdf_url":null,"source":{"id":"https://openalex.org/S189701308","display_name":"Journal of Chemical Theory and Computation","issn_l":"1549-9618","issn":["1549-9618","1549-9626"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Theory and Computation","raw_type":"journal-article"},{"id":"pmid:26574197","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26574197","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical theory and computation","raw_type":"Journal Article"},{"id":"pmh:oai:infoscience.epfl.ch:208426","doi":null,"is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/208426","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I5124864","host_organization_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","host_organization_lineage":["https://openalex.org/I5124864"],"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"},{"id":"pmh:oai:infoscience.tind.io:208426","doi":null,"is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/114513","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I5124864","host_organization_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","host_organization_lineage":["https://openalex.org/I5124864"],"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":null,"raw_type":"research article"}],"best_oa_location":{"id":"pmh:oai:infoscience.epfl.ch:208426","doi":null,"is_oa":true,"landing_page_url":"http://infoscience.epfl.ch/record/208426","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I5124864","host_organization_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","host_organization_lineage":["https://openalex.org/I5124864"],"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"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2338796132","display_name":"Atomistic Basis for the Multiple Functions of the Hsp70 Chaperone Machinery","funder_award_id":"136856","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1513002528","https://openalex.org/W1542579814","https://openalex.org/W1898130445","https://openalex.org/W1966078827","https://openalex.org/W1968438069","https://openalex.org/W1969231606","https://openalex.org/W1969234902","https://openalex.org/W1976499671","https://openalex.org/W1977463239","https://openalex.org/W1978734485","https://openalex.org/W1985070997","https://openalex.org/W1986986500","https://openalex.org/W1989322076","https://openalex.org/W1998091903","https://openalex.org/W2000456051","https://openalex.org/W2006192061","https://openalex.org/W2022175833","https://openalex.org/W2023921624","https://openalex.org/W2027408247","https://openalex.org/W2028875836","https://openalex.org/W2029120587","https://openalex.org/W2031291249","https://openalex.org/W2031593809","https://openalex.org/W2033916002","https://openalex.org/W2034016778","https://openalex.org/W2037159954","https://openalex.org/W2041122953","https://openalex.org/W2043970624","https://openalex.org/W2055936480","https://openalex.org/W2057806291","https://openalex.org/W2060757799","https://openalex.org/W2061270176","https://openalex.org/W2062557777","https://openalex.org/W2071360373","https://openalex.org/W2071827681","https://openalex.org/W2086817352","https://openalex.org/W2112600835","https://openalex.org/W2114296842","https://openalex.org/W2115152262","https://openalex.org/W2119677527","https://openalex.org/W2121374178","https://openalex.org/W2136141445","https://openalex.org/W2141920771","https://openalex.org/W2144288821","https://openalex.org/W2149655632","https://openalex.org/W2151061130","https://openalex.org/W2153058112","https://openalex.org/W2153745204","https://openalex.org/W2157336498","https://openalex.org/W2161605421","https://openalex.org/W2161807210","https://openalex.org/W2162256237","https://openalex.org/W2166098531","https://openalex.org/W2170171286","https://openalex.org/W2317555983","https://openalex.org/W2320400318","https://openalex.org/W2321195257","https://openalex.org/W2327421019","https://openalex.org/W2331494532","https://openalex.org/W2334211226","https://openalex.org/W2335054826","https://openalex.org/W3098919389","https://openalex.org/W4255584963"],"related_works":["https://openalex.org/W2800697076","https://openalex.org/W2583640636","https://openalex.org/W2555870966","https://openalex.org/W3080264551","https://openalex.org/W3125369959","https://openalex.org/W7117162123","https://openalex.org/W2981350008","https://openalex.org/W2997752046","https://openalex.org/W7039433134","https://openalex.org/W2083672523"],"abstract_inverted_index":{"Molecular":[0],"Dynamics":[1],"(MD)":[2],"plays":[3],"a":[4],"fundamental":[5],"role":[6],"in":[7,18,31],"characterizing":[8],"protein":[9],"disordered":[10,33],"states":[11],"that":[12],"are":[13],"emerging":[14],"as":[15],"crucial":[16],"actors":[17],"many":[19],"biological":[20],"processes.":[21],"Here":[22],"we":[23],"assess":[24],"the":[25,69,80],"accuracy":[26],"of":[27],"three":[28],"current":[29],"force-fields":[30,44],"modeling":[32],"peptides":[34],"by":[35,78],"combining":[36],"enhanced-sampling":[37],"MD":[38],"simulations":[39],"with":[40,72],"NMR":[41],"data.":[42],"These":[43],"generate":[45],"significantly":[46],"different":[47],"conformational":[48],"ensembles,":[49],"and":[50,54],"AMBER03w":[51],"[":[52,83],"Best":[53],"Mittal":[55],"J.":[56],"Phys.":[57],"Chem.":[58],"B":[59],"2010":[60,88],",":[61,63,89,91],"114":[62],"14916":[64],"-":[65,93],"14923":[66],"]":[67],"provides":[68],"best":[70],"agreement":[71],"experiments,":[73],"which":[74],"is":[75],"further":[76],"improved":[77],"adding":[79],"ILDN":[81],"corrections":[82],"Lindorff-Larsen":[84],"et":[85],"al.":[86],"Proteins":[87],"78":[90],"1950":[92],"1958":[94],"].":[95]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":15},{"year":2017,"cited_by_count":17},{"year":2016,"cited_by_count":18},{"year":2015,"cited_by_count":14}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
