{"id":"https://openalex.org/W4240300906","doi":"https://doi.org/10.1002/(sici)1097-0134(19980901)32:4<399::aid-prot1>3.3.co;2-h","title":"Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model","display_name":"Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model","publication_year":1998,"publication_date":"1998-09-01","ids":{"openalex":"https://openalex.org/W4240300906","doi":"https://doi.org/10.1002/(sici)1097-0134(19980901)32:4<399::aid-prot1>3.3.co;2-h","mag":"1969405013","pmid":"https://pubmed.ncbi.nlm.nih.gov/9726412"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1097-0134(19980901)32:4<399::aid-prot1>3.3.co;2-h","doi":"https://doi.org/10.1002/(sici)1097-0134(19980901)32:4<399::aid-prot1>3.3.co;2-h","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1097-0134(19980901)32:4<399::aid-prot1>3.3.co;2-h","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Genetics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"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/A5110195908","display_name":"Yury N. Vorobjev","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yury N. Vorobjev","raw_affiliation_strings":["Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062343327","display_name":"Juan Carlos Almagro","orcid":"https://orcid.org/0000-0001-9420-1310","observed_orcids":["https://orcid.org/0000-0001-9420-1310"]},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Juan Carlos Almagro","raw_affiliation_strings":["Instituto de Quimica, Universidad Autonoma de Mexico, Mexico D. F., Mexico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Instituto de Quimica, Universidad Autonoma de Mexico, Mexico D. F., Mexico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109039524","display_name":"Jan Hermans","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jan Hermans","raw_affiliation_strings":["Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina","institution_ids":["https://openalex.org/I114027177"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5110195908"],"corresponding_institution_ids":["https://openalex.org/I114027177"],"apc_list":{"value":4550,"currency":"USD","value_usd":4550},"apc_paid":null,"fwci":3.2942,"has_fulltext":false,"cited_by_count":146,"citation_normalized_percentile":{"value":0.93429763,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"32","issue":"4","first_page":"399","last_page":"413"},"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.000699999975040555,"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/conformational-free-energy","display_name":"conformational free energy","score":0.9430000185966492},{"id":"https://openalex.org/keywords/protein-folding","display_name":"protein folding","score":0.6140000224113464},{"id":"https://openalex.org/keywords/misfolded-proteins","display_name":"misfolded proteins","score":0.753000020980835},{"id":"https://openalex.org/keywords/solvation-free-energy","display_name":"solvation free energy","score":0.8629999756813049},{"id":"https://openalex.org/keywords/dielectric-continuum-model","display_name":"dielectric continuum model","score":0.7760000228881836},{"id":"https://openalex.org/keywords/explicit-solvent-molecular-dynamics","display_name":"explicit solvent molecular dynamics","score":0.7770000100135803},{"id":"https://openalex.org/keywords/conformational-entropy","display_name":"conformational entropy","score":0.7049999833106995},{"id":"https://openalex.org/keywords/poisson-equation","display_name":"Poisson equation","score":0.718999981880188}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7147717475891113},{"id":"https://openalex.org/C2780471494","wikidata":"https://www.wikidata.org/wiki/Q146505","display_name":"Solvent","level":2,"score":0.5781413912773132},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5367909669876099},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.49900221824645996},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.4446990191936493},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4359681308269501},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3566949963569641},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.34415560960769653},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16429686546325684},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.11536332964897156},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1119016706943512},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012997","descriptor_name":"Solvents","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":false}],"locations_count":3,"locations":[{"id":"doi:10.1002/(sici)1097-0134(19980901)32:4<399::aid-prot1>3.3.co;2-h","doi":"https://doi.org/10.1002/(sici)1097-0134(19980901)32:4<399::aid-prot1>3.3.co;2-h","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1097-0134(19980901)32:4<399::aid-prot1>3.3.co;2-h","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Genetics","raw_type":"journal-article"},{"id":"pmid:9726412","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/9726412","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":"Proteins","raw_type":"Journal Article"},{"id":"mag:1969405013","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/9726412","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":null,"is_accepted":false,"is_published":false,"raw_source_name":"PubMed","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":103,"referenced_works":["https://openalex.org/W1502592231","https://openalex.org/W1521867405","https://openalex.org/W1568609060","https://openalex.org/W1572030366","https://openalex.org/W1573009101","https://openalex.org/W1582257194","https://openalex.org/W1589812083","https://openalex.org/W1963737263","https://openalex.org/W1964705595","https://openalex.org/W1965621253","https://openalex.org/W1966867657","https://openalex.org/W1970683586","https://openalex.org/W1972197313","https://openalex.org/W1972772174","https://openalex.org/W1974092275","https://openalex.org/W1974427517","https://openalex.org/W1974507074","https://openalex.org/W1974509391","https://openalex.org/W1975342566","https://openalex.org/W1980028982","https://openalex.org/W1980060705","https://openalex.org/W1980763351","https://openalex.org/W1986252462","https://openalex.org/W1987049547","https://openalex.org/W1987354604","https://openalex.org/W1989171120","https://openalex.org/W1990759970","https://openalex.org/W1992323841","https://openalex.org/W1996054085","https://openalex.org/W1997240546","https://openalex.org/W1997618040","https://openalex.org/W1998708731","https://openalex.org/W1999724806","https://openalex.org/W1999797546","https://openalex.org/W1999938940","https://openalex.org/W2001773296","https://openalex.org/W2003127646","https://openalex.org/W2003381825","https://openalex.org/W2010793745","https://openalex.org/W2011320997","https://openalex.org/W2014140912","https://openalex.org/W2014512733","https://openalex.org/W2028085547","https://openalex.org/W2029615301","https://openalex.org/W2030989748","https://openalex.org/W2033014917","https://openalex.org/W2033350048","https://openalex.org/W2037295961","https://openalex.org/W2038418805","https://openalex.org/W2039015024","https://openalex.org/W2039833566","https://openalex.org/W2041902442","https://openalex.org/W2043429268","https://openalex.org/W2043529199","https://openalex.org/W2047091785","https://openalex.org/W2047840793","https://openalex.org/W2049482544","https://openalex.org/W2050241390","https://openalex.org/W2052017179","https://openalex.org/W2053759741","https://openalex.org/W2058037393","https://openalex.org/W2058806155","https://openalex.org/W2058834481","https://openalex.org/W2063831812","https://openalex.org/W2065456654","https://openalex.org/W2065705570","https://openalex.org/W2065756075","https://openalex.org/W2067291595","https://openalex.org/W2068449210","https://openalex.org/W2071657576","https://openalex.org/W2072073580","https://openalex.org/W2075369230","https://openalex.org/W2076739632","https://openalex.org/W2082296224","https://openalex.org/W2085108537","https://openalex.org/W2085764610","https://openalex.org/W2088189057","https://openalex.org/W2093151204","https://openalex.org/W2093347105","https://openalex.org/W2096264060","https://openalex.org/W2101406819","https://openalex.org/W2102537419","https://openalex.org/W2102849964","https://openalex.org/W2103457811","https://openalex.org/W2108508060","https://openalex.org/W2118157489","https://openalex.org/W2118434640","https://openalex.org/W2120809282","https://openalex.org/W2124044606","https://openalex.org/W2127158652","https://openalex.org/W2132456736","https://openalex.org/W2132589721","https://openalex.org/W2133543883","https://openalex.org/W2140038584","https://openalex.org/W2140387994","https://openalex.org/W2158529871","https://openalex.org/W2161288709","https://openalex.org/W2163906551","https://openalex.org/W2171546617","https://openalex.org/W2177655263","https://openalex.org/W2177731497","https://openalex.org/W4230638849","https://openalex.org/W4235295213"],"related_works":["https://openalex.org/W2085726941","https://openalex.org/W3023274239","https://openalex.org/W2323100538","https://openalex.org/W2765217238","https://openalex.org/W2315248193","https://openalex.org/W7098922790","https://openalex.org/W3033323115","https://openalex.org/W2129783008","https://openalex.org/W2096688676","https://openalex.org/W2171138378"],"abstract_inverted_index":{"A":[0],"new":[1],"method":[2,18,145,283],"for":[3,147,193,203],"calculating":[4],"the":[5,40,50,52,55,61,75,81,84,89,94,102,108,114,124,129,135,137,140,144,149,159,187,206,226,252,286,314],"total":[6],"conformational":[7,287],"free":[8,78,85,116,182,256,288],"energy":[9,44,79,117,179,183,289],"of":[10,20,37,39,60,83,87,93,101,104,113,122,126,128,139,177,195,205,228,251,290,297,302,313],"proteins":[11,298],"in":[12,54,155,311,317],"water":[13,105],"solvent":[14,30,66,106,157],"is":[15,71,231,240],"presented.":[16],"The":[17,64,111,218],"consists":[19],"a":[21,35,120,196,210,275],"relatively":[22],"brief":[23],"simulation":[24,154],"by":[25,58,107],"molecular":[26,141,199,253,267,276],"dynamics":[27,153,277],"with":[28,171,173,225,259],"explicit":[29,156],"(ES)":[31],"molecules":[32],"to":[33,73,167,185,233,284],"produce":[34],"set":[36,301],"microstates":[38],"macroscopic":[41],"conformation.":[42],"Conformational":[43],"and":[45,100,143,162,180,201,220,244,247,271,292,306],"entropy":[46],"are":[47,272],"obtained":[48,308],"from":[49],"simulation,":[51],"latter":[53],"quasi-harmonic":[56],"approximation":[57],"analysis":[59],"covariance":[62],"matrix.":[63],"implicit":[65],"(IS)":[67],"dielectric":[68],"continuum":[69],"model":[70],"used":[72],"calculate":[74,285],"average":[76],"solvation":[77,115,181],"as":[80],"sum":[82],"energies":[86,257],"creating":[88],"solute-size":[90],"hydrophobic":[91],"cavity,":[92],"van":[95],"der":[96],"Waals":[97],"solute-solvent":[98],"interactions,":[99],"polarization":[103],"solute's":[109],"charges.":[110],"reliability":[112],"depends":[118],"on":[119,266],"number":[121,227],"factors:":[123],"details":[125],"arrangement":[127],"protein's":[130,160],"charges,":[131],"especially":[132],"those":[133],"near":[134],"surface;":[136,142],"definition":[138],"chosen":[146],"solving":[148],"Poisson":[150,207],"equation.":[151],"Molecular":[152],"relaxes":[158],"conformation":[161],"allows":[163],"polar":[164],"surface":[165],"groups":[166],"assume":[168],"conformations":[169,296,316],"compatible":[170],"interaction":[172],"solvent,":[174],"while":[175],"averaging":[176],"internal":[178],"tend":[184],"enhance":[186],"precision.":[188],"Two":[189],"recently":[190],"developed":[191],"methods--SIMS,":[192],"calculation":[194],"smooth":[197],"invariant":[198],"surface,":[200],"FAMBE,":[202],"solution":[204],"equation":[208],"via":[209],"fast":[211],"adaptive":[212],"multigrid":[213],"boundary":[214],"element--have":[215],"been":[216],"employed.":[217],"SIMS":[219,230],"FAMBE":[221],"programs":[222,262],"scale":[223],"linearly":[224],"atoms.":[229],"superior":[232],"Connolly's":[234],"MS":[235],"(molecular":[236],"surface)":[237],"program:":[238],"it":[239,248],"faster,":[241],"more":[242,245],"accurate,":[243],"stable,":[246],"smooths":[249],"singularities":[250],"surface.":[254],"Solvation":[255],"calculated":[258],"these":[260],"two":[261],"do":[263],"not":[264],"depend":[265],"position":[268],"or":[269],"orientation":[270],"stable":[273],"along":[274],"trajectory.":[278],"We":[279],"have":[280,307],"applied":[281],"this":[282],"native":[291,315],"intentionally":[293],"misfolded":[294,304],"globular":[295],"(the":[299],"EMBL":[300],"deliberately":[303],"proteins)":[305],"good":[309],"discrimination":[310],"favor":[312],"all":[318],"instances.":[319]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":6}],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2022-05-12T00:00:00"}
