{"id":"https://openalex.org/W1977312918","doi":"https://doi.org/10.1063/1.2757172","title":"Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide","display_name":"Sampling of states for estimating the folding funnel entropy and energy landscape of a model alpha-helical hairpin peptide","publication_year":2007,"publication_date":"2007-08-17","ids":{"openalex":"https://openalex.org/W1977312918","doi":"https://doi.org/10.1063/1.2757172","mag":"1977312918","pmid":"https://pubmed.ncbi.nlm.nih.gov/17718634"},"language":"en","primary_location":{"id":"doi:10.1063/1.2757172","doi":"https://doi.org/10.1063/1.2757172","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.2757172","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","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/A5071186045","display_name":"Prem P. Chapagain","orcid":"https://orcid.org/0000-0002-0999-4975","observed_orcids":["https://orcid.org/0000-0002-0999-4975"]},"institutions":[{"id":"https://openalex.org/I19700959","display_name":"Florida International University","ror":"https://ror.org/02gz6gg07","country_code":"US","type":"education","lineage":["https://openalex.org/I19700959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Prem P. Chapagain","raw_affiliation_strings":["Florida International University Department of Physics, , University Park, Miami, Florida 33199"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida International University Department of Physics, , University Park, Miami, Florida 33199","institution_ids":["https://openalex.org/I19700959"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jose L. Parra","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I19700959","display_name":"Florida International University","ror":"https://ror.org/02gz6gg07","country_code":"US","type":"education","lineage":["https://openalex.org/I19700959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jose L. Parra","raw_affiliation_strings":["Florida International University Department of Physics, , University Park, Miami, Florida 33199"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida International University Department of Physics, , University Park, Miami, Florida 33199","institution_ids":["https://openalex.org/I19700959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063623074","display_name":"Bernard S. Gerstman","orcid":"https://orcid.org/0000-0003-4258-529X","observed_orcids":["https://orcid.org/0000-0003-4258-529X"]},"institutions":[{"id":"https://openalex.org/I19700959","display_name":"Florida International University","ror":"https://ror.org/02gz6gg07","country_code":"US","type":"education","lineage":["https://openalex.org/I19700959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bernard S. Gerstman","raw_affiliation_strings":["Florida International University Department of Physics, , University Park, Miami, Florida 33199"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida International University Department of Physics, , University Park, Miami, Florida 33199","institution_ids":["https://openalex.org/I19700959"]}]},{"author_position":"last","author":{"id":null,"display_name":"Yanxin Liu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I19700959","display_name":"Florida International University","ror":"https://ror.org/02gz6gg07","country_code":"US","type":"education","lineage":["https://openalex.org/I19700959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yanxin Liu","raw_affiliation_strings":["Florida International University Department of Physics, , University Park, Miami, Florida 33199"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida International University Department of Physics, , University Park, Miami, Florida 33199","institution_ids":["https://openalex.org/I19700959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I19700959"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":null,"fwci":1.1913,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.75383851,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"127","issue":"7","first_page":"075103","last_page":"075103"},"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":0.0010000000474974513,"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":9.999999747378752e-05,"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":0.8169999718666077},{"id":"https://openalex.org/keywords/folding-funnel","display_name":"folding funnel","score":0.8960000276565552},{"id":"https://openalex.org/keywords/energy-landscape","display_name":"energy landscape","score":0.8500000238418579},{"id":"https://openalex.org/keywords/entropy","display_name":"entropy","score":0.6499999761581421},{"id":"https://openalex.org/keywords/peptides","display_name":"peptides","score":0.40799999237060547},{"id":"https://openalex.org/keywords/lattice-model","display_name":"lattice model","score":0.5460000038146973},{"id":"https://openalex.org/keywords/state-counting","display_name":"state counting","score":0.7360000014305115},{"id":"https://openalex.org/keywords/random-coil","display_name":"random coil","score":0.8410000205039978},{"id":"https://openalex.org/keywords/protein-folding-rate","display_name":"folding rate","score":0.4390000104904175},{"id":"https://openalex.org/keywords/thermodynamics-of-folding","display_name":"thermodynamics of folding","score":0.5569999814033508}],"concepts":[{"id":"https://openalex.org/C17435862","wikidata":"https://www.wikidata.org/wiki/Q29957","display_name":"Funnel","level":2,"score":0.9004237055778503},{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.7282520532608032},{"id":"https://openalex.org/C46449900","wikidata":"https://www.wikidata.org/wiki/Q5303170","display_name":"Downhill folding","level":4,"score":0.5924901962280273},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.5580155849456787},{"id":"https://openalex.org/C206276672","wikidata":"https://www.wikidata.org/wiki/Q5164839","display_name":"Contact order","level":3,"score":0.5299065113067627},{"id":"https://openalex.org/C174507519","wikidata":"https://www.wikidata.org/wiki/Q5464306","display_name":"Folding funnel","level":5,"score":0.5180649757385254},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5136896967887878},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.5038475394248962},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.4843081533908844},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.4780716896057129},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4528818428516388},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35649043321609497},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.30206751823425293},{"id":"https://openalex.org/C162203774","wikidata":"https://www.wikidata.org/wiki/Q7181581","display_name":"Phi value analysis","level":3,"score":0.22775939106941223},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2046557366847992},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1907503604888916},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.1318836808204651},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11474356055259705},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.09804239869117737},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.09697353839874268},{"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/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","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":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","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":"D008962","descriptor_name":"Models, Theoretical","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1063/1.2757172","doi":"https://doi.org/10.1063/1.2757172","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.2757172","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},{"id":"pmid:17718634","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17718634","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 chemical physics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1600015000","https://openalex.org/W1963871440","https://openalex.org/W1973488611","https://openalex.org/W1984527736","https://openalex.org/W1986155795","https://openalex.org/W1991106926","https://openalex.org/W2000490321","https://openalex.org/W2001818491","https://openalex.org/W2008713184","https://openalex.org/W2013319266","https://openalex.org/W2014095962","https://openalex.org/W2021510290","https://openalex.org/W2024466362","https://openalex.org/W2025507051","https://openalex.org/W2028841335","https://openalex.org/W2032008622","https://openalex.org/W2032704124","https://openalex.org/W2041721370","https://openalex.org/W2045439785","https://openalex.org/W2046824192","https://openalex.org/W2049238377","https://openalex.org/W2058067565","https://openalex.org/W2058900154","https://openalex.org/W2064810205","https://openalex.org/W2068693928","https://openalex.org/W2072325285","https://openalex.org/W2073656584","https://openalex.org/W2075488737","https://openalex.org/W2076488922","https://openalex.org/W2082729655","https://openalex.org/W2083921490","https://openalex.org/W2092357419","https://openalex.org/W2092424728","https://openalex.org/W2108523880","https://openalex.org/W2132897636","https://openalex.org/W2145010489","https://openalex.org/W2157187121","https://openalex.org/W2158476854","https://openalex.org/W2159669148","https://openalex.org/W2171755502","https://openalex.org/W2236569259","https://openalex.org/W3100532415","https://openalex.org/W3104316942"],"related_works":["https://openalex.org/W1578644236","https://openalex.org/W1996679245","https://openalex.org/W1618940275","https://openalex.org/W2143268609","https://openalex.org/W2041721370","https://openalex.org/W1982421433","https://openalex.org/W2087746064","https://openalex.org/W2085516197","https://openalex.org/W2169309877","https://openalex.org/W2105903067"],"abstract_inverted_index":{"Protein":[0],"folding":[1,24,42,141],"times":[2],"are":[3],"many":[4],"orders":[5],"of":[6,32,41,51,54,66,76,98,106,135,161,164,171],"magnitude":[7],"shorter":[8],"than":[9],"would":[10],"occur":[11],"if":[12],"the":[13,37,44,48,89,104,131,136,150,158,165,169,172],"peptide":[14],"chain":[15],"randomly":[16],"sampled":[17],"possible":[18,107],"configurations,":[19],"which":[20],"implies":[21],"that":[22,60,75,152],"protein":[23,99],"is":[25,61,74],"a":[26,140],"directed":[27],"process.":[28],"The":[29],"detailed":[30],"shape":[31],"protein's":[33],"energy":[34,58,78,83,91,134,137],"landscape":[35,59,138],"determines":[36],"rate":[38],"and":[39,117,133],"reliability":[40],"to":[43,63,88,112,122,129,156],"native":[45,92],"state,":[46],"but":[47],"large":[49,111],"number":[50,105,160],"structural":[52],"degrees":[53],"freedom":[55],"generates":[56],"an":[57,77,126,144],"hard":[62],"visualize":[64],"because":[65],"its":[67],"high":[68,82],"dimensionality.":[69],"A":[70],"commonly":[71],"used":[72],"picture":[73],"funnel":[79,142],"leading":[80],"from":[81],"random":[84,166],"coil":[85,167],"state":[86],"down":[87],"low":[90],"state.":[93],"As":[94],"lattice":[95],"computer":[96],"models":[97],"dynamics":[100],"become":[101],"more":[102],"realistic,":[103],"configurations":[108],"becomes":[109],"too":[110],"count":[113,123,157],"directly.":[114],"Statistical":[115],"mechanic":[116],"thermodynamic":[118],"approaches":[119],"allow":[120],"us":[121],"states":[124,163],"in":[125,154],"approximate":[127],"manner":[128],"quantify":[130],"entropy":[132],"within":[139],"for":[143],"alpha-helical":[145],"protein.":[146],"We":[147],"also":[148],"discuss":[149],"problems":[151],"arise":[153],"attempting":[155],"huge":[159],"individual":[162],"at":[168],"top":[170],"funnel.":[173]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
