{"id":"https://openalex.org/W2008403856","doi":"https://doi.org/10.1021/jp990851x","title":"The Thermodynamics and Kinetics of Protein Folding: A Lattice Model Analysis of Multiple Pathways with Intermediates","display_name":"The Thermodynamics and Kinetics of Protein Folding: A Lattice Model Analysis of Multiple Pathways with Intermediates","publication_year":1999,"publication_date":"1999-08-31","ids":{"openalex":"https://openalex.org/W2008403856","doi":"https://doi.org/10.1021/jp990851x","mag":"2008403856"},"language":"en","primary_location":{"id":"doi:10.1021/jp990851x","doi":"https://doi.org/10.1021/jp990851x","is_oa":false,"landing_page_url":"https://doi.org/10.1021/jp990851x","pdf_url":null,"source":{"id":"https://openalex.org/S185621672","display_name":"The Journal of Physical Chemistry B","issn_l":"1520-5207","issn":["1520-5207","1520-6106"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-140","russia-white-list-2","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":"The Journal of Physical Chemistry B","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075498364","display_name":"Aaron R. Dinner","orcid":"https://orcid.org/0000-0001-8328-6427","observed_orcids":["https://orcid.org/0000-0001-8328-6427"]},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron R. Dinner","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts 02138, and Laboratoire de Chimie Biophysique, Institut le Bel, Universit\u00e9 Louis Pasteur, 4 Rue Blaise Pascal, 67000 Strasbourg, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts 02138, and Laboratoire de Chimie Biophysique, Institut le Bel, Universit\u00e9 Louis Pasteur, 4 Rue Blaise Pascal, 67000 Strasbourg, France","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076499540","display_name":"Martin Karplus","orcid":"https://orcid.org/0000-0002-5485-6117","observed_orcids":["https://orcid.org/0000-0002-5485-6117"]},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin Karplus","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts 02138, and Laboratoire de Chimie Biophysique, Institut le Bel, Universit\u00e9 Louis Pasteur, 4 Rue Blaise Pascal, 67000 Strasbourg, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, Massachusetts 02138, and Laboratoire de Chimie Biophysique, Institut le Bel, Universit\u00e9 Louis Pasteur, 4 Rue Blaise Pascal, 67000 Strasbourg, France","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I136199984"],"apc_list":null,"apc_paid":null,"fwci":2.7386,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.90524713,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"103","issue":"37","first_page":"7976","last_page":"7994"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980000257492065,"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":0.9980000257492065,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.000699999975040555,"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":0.00019999999494757503,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-folding","display_name":"protein folding","score":0.984000027179718},{"id":"https://openalex.org/keywords/folding-kinetics","display_name":"folding kinetics","score":0.8360000252723694},{"id":"https://openalex.org/keywords/folding-thermodynamics","display_name":"folding thermodynamics","score":0.9779999852180481},{"id":"https://openalex.org/keywords/folding-intermediates","display_name":"folding intermediates","score":0.7850000262260437},{"id":"https://openalex.org/keywords/lattice-model","display_name":"lattice model","score":0.6010000109672546},{"id":"https://openalex.org/keywords/simple-cubic-lattice","display_name":"simple cubic lattice","score":0.7419999837875366},{"id":"https://openalex.org/keywords/monte-carlo-dynamics","display_name":"Monte Carlo dynamics","score":0.6269999742507935},{"id":"https://openalex.org/keywords/transition-state","display_name":"transition state","score":0.7620000243186951},{"id":"https://openalex.org/keywords/folding-pathways","display_name":"folding pathways","score":0.6169999837875366},{"id":"https://openalex.org/keywords/core-formation","display_name":"core formation","score":0.6710000038146973},{"id":"https://openalex.org/keywords/density-of-states","display_name":"density of states","score":0.8209999799728394},{"id":"https://openalex.org/keywords/free-energy","display_name":"free energy","score":0.7179999947547913},{"id":"https://openalex.org/keywords/lysozyme","display_name":"lysozyme","score":0.7120000123977661},{"id":"https://openalex.org/keywords/protein-folding-mechanism","display_name":"protein folding mechanism","score":0.4230000078678131}],"concepts":[{"id":"https://openalex.org/C148898269","wikidata":"https://www.wikidata.org/wiki/Q1108792","display_name":"Kinetics","level":2,"score":0.7184473872184753},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.6265565156936646},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5540265440940857},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.48125407099723816},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4451253116130829},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23196899890899658},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1474784016609192},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1021/jp990851x","doi":"https://doi.org/10.1021/jp990851x","is_oa":false,"landing_page_url":"https://doi.org/10.1021/jp990851x","pdf_url":null,"source":{"id":"https://openalex.org/S185621672","display_name":"The Journal of Physical Chemistry B","issn_l":"1520-5207","issn":["1520-5207","1520-6106"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-140","russia-white-list-2","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":"The Journal of Physical Chemistry B","raw_type":"journal-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.715.8160","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.715.8160","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://dinner-group.uchicago.edu/mypdf/1999/JPC103.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":69,"referenced_works":["https://openalex.org/W1550166367","https://openalex.org/W1963688013","https://openalex.org/W1966521026","https://openalex.org/W1966616271","https://openalex.org/W1967235874","https://openalex.org/W1968998311","https://openalex.org/W1969533855","https://openalex.org/W1970440715","https://openalex.org/W1975682842","https://openalex.org/W1976271045","https://openalex.org/W1976601752","https://openalex.org/W1978885914","https://openalex.org/W1979038840","https://openalex.org/W1980045457","https://openalex.org/W1982006129","https://openalex.org/W1982338804","https://openalex.org/W1986466512","https://openalex.org/W1988176696","https://openalex.org/W1988529738","https://openalex.org/W1988690429","https://openalex.org/W1999270898","https://openalex.org/W2003171997","https://openalex.org/W2005865331","https://openalex.org/W2008713184","https://openalex.org/W2008818819","https://openalex.org/W2009467983","https://openalex.org/W2009513422","https://openalex.org/W2010703720","https://openalex.org/W2012298149","https://openalex.org/W2014798121","https://openalex.org/W2015816091","https://openalex.org/W2016019576","https://openalex.org/W2017212707","https://openalex.org/W2020563037","https://openalex.org/W2020565933","https://openalex.org/W2022231452","https://openalex.org/W2025127982","https://openalex.org/W2027845731","https://openalex.org/W2028702957","https://openalex.org/W2029057661","https://openalex.org/W2036846189","https://openalex.org/W2041661865","https://openalex.org/W2044483297","https://openalex.org/W2046152827","https://openalex.org/W2049092553","https://openalex.org/W2056211756","https://openalex.org/W2056760934","https://openalex.org/W2067323731","https://openalex.org/W2069479024","https://openalex.org/W2072417182","https://openalex.org/W2076803651","https://openalex.org/W2078067862","https://openalex.org/W2078362254","https://openalex.org/W2079606633","https://openalex.org/W2080122947","https://openalex.org/W2080449760","https://openalex.org/W2081810556","https://openalex.org/W2085479332","https://openalex.org/W2088397672","https://openalex.org/W2102352058","https://openalex.org/W2104533058","https://openalex.org/W2107100181","https://openalex.org/W2110043143","https://openalex.org/W2138758230","https://openalex.org/W2142834594","https://openalex.org/W2144625378","https://openalex.org/W2145010489","https://openalex.org/W2888544893","https://openalex.org/W2993880730"],"related_works":["https://openalex.org/W2008713184","https://openalex.org/W1968827368","https://openalex.org/W2107100181","https://openalex.org/W2137583795","https://openalex.org/W4244542764","https://openalex.org/W2042648542","https://openalex.org/W2165222310","https://openalex.org/W2466548032","https://openalex.org/W1569560802","https://openalex.org/W2083505922"],"abstract_inverted_index":{"The":[0,27,108,221,253],"kinetics":[1],"and":[2,65,79,119,134,167,178,204,213],"thermodynamics":[3,222],"of":[4,6,10,44,121,125,131,145,165,175,202,217,255,272],"folding":[5,112,166,257],"a":[7,11,21,40,47,55,84,122,163,188,260,269],"representative":[8],"sequence":[9],"125-residue":[12],"protein":[13,271],"model":[14],"subject":[15],"to":[16,32,61,83,91,235,263],"Monte":[17,192],"Carlo":[18,193],"dynamics":[19,117],"on":[20,162],"simple":[22],"cubic":[23],"lattice":[24],"were":[25],"investigated.":[26],"diverse":[28],"trajectories":[29],"that":[30,58,147],"lead":[31],"the":[33,52,62,75,81,89,92,126,129,156,173,176,179,183,200,209,218,228,231,240,244,256],"native":[34,63,93],"state":[35,64,94,110],"can":[36,148],"be":[37,149],"classified":[38],"into":[39],"relatively":[41],"small":[42],"number":[43],"average":[45],"pathways:":[46],"\u201cfast":[48],"track\u201d":[49],"in":[50,69,128,187,224,239],"which":[51,70,103,137],"chain":[53,82,184],"forms":[54],"stable":[56,101],"core":[57,76,127,177],"folds":[59],"directly":[60],"several":[66],"\u201cslow":[67],"tracks\u201d":[68],"particular":[71],"contacts":[72,136],"form":[73],"before":[74],"is":[77,95,113,185],"complete":[78],"direct":[80],"misfolded":[85],"intermediate.":[86,190],"Rearrangement":[87],"from":[88],"intermediates":[90,245],"slow":[96,138],"because":[97],"it":[98],"requires":[99],"breaking":[100],"contacts,":[102],"involve":[104],"primarily":[105],"surface":[106],"residues.":[107],"transition":[109,232],"for":[111,155,199,267],"identified":[114],"by":[115,151],"activated":[116],"simulations":[118],"consists":[120],"reduced":[123],"version":[124],"absence":[130],"other":[132,180],"(native":[133],"nonnative)":[135],"folding.":[139],"Each":[140],"track":[141],"involves":[142],"an":[143,197],"ensemble":[144],"structures":[146],"characterized":[150],"two":[152,219],"progress":[153],"coordinates":[154,159],"reaction.":[157],"These":[158],"are":[160,223,246],"based":[161],"comparison":[164],"nonfolding":[168],"trajectories:":[169],"one":[170],"coordinate":[171],"monitors":[172,181],"formation":[174],"whether":[182],"trapped":[186],"long-lived":[189],"From":[191],"simulations,":[194],"we":[195],"obtain":[196],"estimate":[198],"density":[201],"states":[203,233],"calculate":[205],"equilibrium":[206],"averages,":[207],"including":[208],"free":[210,241,250],"energy,":[211,212],"entropy,":[214],"as":[215],"functions":[216],"coordinates.":[220],"good":[225],"agreement":[226],"with":[227],"observed":[229,265],"kinetics;":[230],"correspond":[234],"plateaus":[236],"or":[237],"barriers":[238],"energy":[242,251],"while":[243],"energetically":[247],"stabilized":[248],"local":[249],"minima.":[252],"complexities":[254],"mechanism":[258],"bear":[259],"striking":[261],"similarity":[262],"those":[264],"experimentally":[266],"lysozyme,":[268],"well-studied":[270],"comparable":[273],"size.":[274]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-10-08T09:06:37.294493","created_date":"2016-06-24T00:00:00"}
