{"id":"https://openalex.org/W2055775600","doi":"https://doi.org/10.1021/jp102575b","title":"Balance between \u03b1 and \u03b2 Structures in Ab Initio Protein Folding","display_name":"Balance between \u03b1 and \u03b2 Structures in Ab Initio Protein Folding","publication_year":2010,"publication_date":"2010-06-10","ids":{"openalex":"https://openalex.org/W2055775600","doi":"https://doi.org/10.1021/jp102575b","mag":"2055775600","pmid":"https://pubmed.ncbi.nlm.nih.gov/20536262"},"language":"en","primary_location":{"id":"doi:10.1021/jp102575b","doi":"https://doi.org/10.1021/jp102575b","is_oa":false,"landing_page_url":"https://doi.org/10.1021/jp102575b","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","pubmed"],"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/A5059620610","display_name":"Robert B. Best","orcid":"https://orcid.org/0000-0002-7893-3543","observed_orcids":["https://orcid.org/0000-0002-7893-3543"]},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]},{"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","US"],"is_corresponding":true,"raw_author_name":"Robert B. Best","raw_affiliation_strings":["Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania","institution_ids":["https://openalex.org/I186143895","https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088540108","display_name":"Jeetain Mittal","orcid":"https://orcid.org/0000-0002-9725-6402","observed_orcids":["https://orcid.org/0000-0002-9725-6402"]},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]},{"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","US"],"is_corresponding":true,"raw_author_name":"Jeetain Mittal","raw_affiliation_strings":["Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K., and Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania","institution_ids":["https://openalex.org/I186143895","https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5059620610","https://openalex.org/A5088540108"],"corresponding_institution_ids":["https://openalex.org/I186143895","https://openalex.org/I241749"],"apc_list":null,"apc_paid":null,"fwci":4.7364,"has_fulltext":false,"cited_by_count":111,"citation_normalized_percentile":{"value":0.96495188,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"114","issue":"26","first_page":"8790","last_page":"8798"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":9.999999747378752e-05,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-folding","display_name":"protein folding","score":0.9700000286102295},{"id":"https://openalex.org/keywords/force-field-optimization","display_name":"force field optimization","score":0.6909999847412109},{"id":"https://openalex.org/keywords/alpha-helix","display_name":"alpha-helix","score":0.6019999980926514},{"id":"https://openalex.org/keywords/beta-sheet","display_name":"beta-sheet","score":0.9269999861717224},{"id":"https://openalex.org/keywords/secondary-structure-propensity","display_name":"secondary structure propensity","score":0.5960000157356262},{"id":"https://openalex.org/keywords/replica-exchange-molecular-dynamics","display_name":"replica exchange molecular dynamics","score":0.8349999785423279}],"concepts":[{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.7516814470291138},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.6327522993087769},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.6206813454627991},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.610192596912384},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.5415461659431458},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.5186256766319275},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5105446577072144},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5104004740715027},{"id":"https://openalex.org/C174507519","wikidata":"https://www.wikidata.org/wiki/Q5464306","display_name":"Folding funnel","level":5,"score":0.5068069100379944},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.49184513092041016},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.4492630958557129},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.44588789343833923},{"id":"https://openalex.org/C19472624","wikidata":"https://www.wikidata.org/wiki/Q583851","display_name":"Native state","level":2,"score":0.42693957686424255},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.42341727018356323},{"id":"https://openalex.org/C46449900","wikidata":"https://www.wikidata.org/wiki/Q5303170","display_name":"Downhill folding","level":4,"score":0.39938652515411377},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3021048903465271},{"id":"https://openalex.org/C162203774","wikidata":"https://www.wikidata.org/wiki/Q7181581","display_name":"Phi value analysis","level":3,"score":0.2957614064216614},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.2209167182445526},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.12884485721588135},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.10464045405387878},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009682","descriptor_name":"Magnetic Resonance Spectroscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011489","descriptor_name":"Protein Denaturation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","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":"D031541","descriptor_name":"Fluorescence Resonance Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/jp102575b","doi":"https://doi.org/10.1021/jp102575b","is_oa":false,"landing_page_url":"https://doi.org/10.1021/jp102575b","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":"pmid:20536262","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20536262","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":"The journal of physical chemistry. B","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":87,"referenced_works":["https://openalex.org/W192510599","https://openalex.org/W1658649599","https://openalex.org/W1960408443","https://openalex.org/W1966078827","https://openalex.org/W1966712500","https://openalex.org/W1966743338","https://openalex.org/W1969231606","https://openalex.org/W1976499671","https://openalex.org/W1979018519","https://openalex.org/W1979716756","https://openalex.org/W1981021420","https://openalex.org/W1984332755","https://openalex.org/W1985070997","https://openalex.org/W1990606222","https://openalex.org/W1991329443","https://openalex.org/W1992422451","https://openalex.org/W1994239510","https://openalex.org/W1995156107","https://openalex.org/W1997362265","https://openalex.org/W2000625121","https://openalex.org/W2006520052","https://openalex.org/W2008850469","https://openalex.org/W2016838955","https://openalex.org/W2017394797","https://openalex.org/W2018312454","https://openalex.org/W2018657646","https://openalex.org/W2020716464","https://openalex.org/W2021662557","https://openalex.org/W2022982893","https://openalex.org/W2023921624","https://openalex.org/W2027854802","https://openalex.org/W2030761972","https://openalex.org/W2031273789","https://openalex.org/W2035211954","https://openalex.org/W2035247582","https://openalex.org/W2035995793","https://openalex.org/W2040809566","https://openalex.org/W2042947255","https://openalex.org/W2043294570","https://openalex.org/W2046379303","https://openalex.org/W2047510784","https://openalex.org/W2049054862","https://openalex.org/W2051633053","https://openalex.org/W2056975402","https://openalex.org/W2058198562","https://openalex.org/W2058881180","https://openalex.org/W2061844749","https://openalex.org/W2062338207","https://openalex.org/W2065919348","https://openalex.org/W2066010782","https://openalex.org/W2066041565","https://openalex.org/W2066358752","https://openalex.org/W2069123478","https://openalex.org/W2069288013","https://openalex.org/W2072290134","https://openalex.org/W2078515575","https://openalex.org/W2081338193","https://openalex.org/W2081760211","https://openalex.org/W2081926098","https://openalex.org/W2082459114","https://openalex.org/W2085146429","https://openalex.org/W2087356905","https://openalex.org/W2089258285","https://openalex.org/W2093221728","https://openalex.org/W2095911937","https://openalex.org/W2101247857","https://openalex.org/W2104414143","https://openalex.org/W2105900744","https://openalex.org/W2110113231","https://openalex.org/W2117134841","https://openalex.org/W2122220546","https://openalex.org/W2123768693","https://openalex.org/W2133294519","https://openalex.org/W2137714390","https://openalex.org/W2137841361","https://openalex.org/W2140340353","https://openalex.org/W2142578757","https://openalex.org/W2144288821","https://openalex.org/W2145326890","https://openalex.org/W2152899104","https://openalex.org/W2153970368","https://openalex.org/W2159923313","https://openalex.org/W2161447192","https://openalex.org/W2162319691","https://openalex.org/W2164011287","https://openalex.org/W2275670374","https://openalex.org/W2319226565"],"related_works":["https://openalex.org/W2016140764","https://openalex.org/W1980115689","https://openalex.org/W2056305863","https://openalex.org/W2106560147","https://openalex.org/W2037673752","https://openalex.org/W2051982935","https://openalex.org/W2077409321","https://openalex.org/W2128750516","https://openalex.org/W2806226382","https://openalex.org/W2135860334"],"abstract_inverted_index":{"Despite":[0],"initial":[1],"successes":[2],"in":[3,79,104,131,171],"folding":[4,50,180],"of":[5,34,43,51,68,181],"proteins":[6,182],"by":[7,39],"molecular":[8,87],"simulation,":[9],"it":[10],"is":[11,37,176],"becoming":[12],"increasingly":[13],"evident":[14],"that":[15,31,147,166,175],"current":[16],"energy":[17],"functions":[18],"(force":[19],"fields)":[20],"tend":[21],"to":[22,75,138,178],"favor":[23],"either":[24,54],"alpha":[25,56],"or":[26,59],"beta":[27,60],"secondary":[28],"structure,":[29],"such":[30],"the":[32,40,44,49,69,97,108,149,155,167,179],"choice":[33],"force":[35,72,173],"field":[36,174],"governed":[38],"structural":[41,77,185],"class":[42],"protein.":[45],"Here,":[46],"we":[47,95],"study":[48],"peptides":[52],"with":[53,64,107,122,134],"predominantly":[55],"(Trp":[57],"cage)":[58],"(GB1":[61],"hairpin)":[62],"structure":[63,100,111],"a":[65,80,172],"modified":[66],"version":[67],"Amber":[70],"ff03":[71],"field,":[73],"optimized":[74],"reproduce":[76],"propensity":[78],"helix-forming":[81],"peptide.":[82],"Using":[83],"extensive":[84],"replica":[85],"exchange":[86],"dynamics":[88],"simulations":[89],"starting":[90],"from":[91,141,183],"completely":[92],"unfolded":[93,156],"configurations,":[94],"obtain":[96,118],"correct":[98],"folded":[99,123,150],"for":[101],"each":[102],"peptide,":[103],"close":[105],"agreement":[106],"experimental":[109,139],"native":[110],"(<1.5":[112],"A":[113],"all-atom":[114],"root-mean-square":[115],"deviation).":[116],"We":[117],"converged":[119],"equilibrium":[120],"distributions,":[121],"populations":[124],"at":[125],"standard":[126],"conditions":[127],"(approximately":[128],"300":[129],"K),":[130],"remarkable":[132],"accord":[133],"experiment.":[135],"Further":[136],"comparison":[137],"data":[140],"NMR":[142],"spectroscopy":[143],"and":[144,161],"FRET":[145],"suggests":[146],"although":[148],"structures":[151],"are":[152],"accurately":[153],"reproduced,":[154],"state":[157],"remains":[158],"too":[159],"structured":[160],"compact.":[162],"Our":[163],"results":[164,170],"suggest":[165],"backbone":[168],"correction":[169],"transferable":[177],"different":[184],"classes.":[186]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":4},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":10},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":15},{"year":2012,"cited_by_count":19}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
