{"id":"https://openalex.org/W2071377225","doi":"https://doi.org/10.1002/(sici)1096-987x(19991130)20:15<1644::aid-jcc5>3.0.co;2-y","title":"Efficient calculation of two-dimensional adiabatic and free energy maps: Application to the isomerization of the C13?C14 and C15?N16 bonds in the retinal of bacteriorhodopsin","display_name":"Efficient calculation of two-dimensional adiabatic and free energy maps: Application to the isomerization of the C13?C14 and C15?N16 bonds in the retinal of bacteriorhodopsin","publication_year":1999,"publication_date":"1999-11-30","ids":{"openalex":"https://openalex.org/W2071377225","doi":"https://doi.org/10.1002/(sici)1096-987x(19991130)20:15<1644::aid-jcc5>3.0.co;2-y","mag":"2071377225"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1096-987x(19991130)20:15<1644::aid-jcc5>3.0.co;2-y","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19991130)20:15<1644::aid-jcc5>3.0.co;2-y","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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":"Journal of Computational Chemistry","raw_type":"journal-article"},"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/A5082211391","display_name":"Serge Crouzy","orcid":"https://orcid.org/0000-0001-5586-113X"},"institutions":[{"id":"https://openalex.org/I2738703131","display_name":"Commissariat \u00e0 l'\u00c9nergie Atomique et aux \u00c9nergies Alternatives","ror":"https://ror.org/00jjx8s55","country_code":"FR","type":"funder","lineage":["https://openalex.org/I2738703131"]},{"id":"https://openalex.org/I3020098449","display_name":"CEA Grenoble","ror":"https://ror.org/02mg6n827","country_code":"FR","type":"government","lineage":["https://openalex.org/I2738703131","https://openalex.org/I3020098449"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Serge Crouzy","raw_affiliation_strings":["BMC DBMS CEA, 17, rue des Martyrs, 38054 Grenoble cedex 9, France"],"affiliations":[{"raw_affiliation_string":"BMC DBMS CEA, 17, rue des Martyrs, 38054 Grenoble cedex 9, France","institution_ids":["https://openalex.org/I3020098449","https://openalex.org/I2738703131"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109184116","display_name":"Jer\ufffdme Baudry","orcid":null},"institutions":[{"id":"https://openalex.org/I2738703131","display_name":"Commissariat \u00e0 l'\u00c9nergie Atomique et aux \u00c9nergies Alternatives","ror":"https://ror.org/00jjx8s55","country_code":"FR","type":"funder","lineage":["https://openalex.org/I2738703131"]},{"id":"https://openalex.org/I4210128565","display_name":"CEA Paris-Saclay","ror":"https://ror.org/03n15ch10","country_code":"FR","type":"government","lineage":["https://openalex.org/I2738703131","https://openalex.org/I277688954","https://openalex.org/I4210128565"]},{"id":"https://openalex.org/I2801360556","display_name":"CEA Paris-Saclay - Etablissement de Saclay","ror":"https://ror.org/01fv25t22","country_code":"FR","type":"facility","lineage":["https://openalex.org/I2738703131","https://openalex.org/I277688954","https://openalex.org/I2801360556","https://openalex.org/I4210128565"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jer\ufffdme Baudry","raw_affiliation_strings":["CEA Saclay, France"],"affiliations":[{"raw_affiliation_string":"CEA Saclay, France","institution_ids":["https://openalex.org/I2801360556","https://openalex.org/I4210128565","https://openalex.org/I2738703131"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018366869","display_name":"Jeremy C. Smith","orcid":"https://orcid.org/0000-0002-2978-3227"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jeremy C. Smith","raw_affiliation_strings":["Lehrstuhl fu\u0308r Biocomputing, IWR Universita\u0308t Heidelberg, Im Neuenheiner Feld 368, D-69120 Heidelberg, Germany","Lehrstuhl f\u00fcr Biocomputing, IWR Universit\u00e4t Heidelberg, Im Neuenheiner Feld 368, D\u201069120 Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Lehrstuhl fu\u0308r Biocomputing, IWR Universita\u0308t Heidelberg, Im Neuenheiner Feld 368, D-69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]},{"raw_affiliation_string":"Lehrstuhl f\u00fcr Biocomputing, IWR Universit\u00e4t Heidelberg, Im Neuenheiner Feld 368, D\u201069120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110138583","display_name":"Beno\ufffdt Roux","orcid":null},"institutions":[{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Beno\ufffdt Roux","raw_affiliation_strings":["Chemistry Department, Universite\u0301 de Montre\u0301al, C.P. 6128, succ. A, Montre\u0301al, Canada H3C 3J7","Chemistry Department, Universit\u00e9 de Montr\u00e9al, C.P. 6128, succ. A, Montr\u00e9al, Canada H3C 3J7"],"affiliations":[{"raw_affiliation_string":"Chemistry Department, Universite\u0301 de Montre\u0301al, C.P. 6128, succ. A, Montre\u0301al, Canada H3C 3J7","institution_ids":["https://openalex.org/I70931966"]},{"raw_affiliation_string":"Chemistry Department, Universit\u00e9 de Montr\u00e9al, C.P. 6128, succ. A, Montr\u00e9al, Canada H3C 3J7","institution_ids":["https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5082211391"],"corresponding_institution_ids":["https://openalex.org/I2738703131","https://openalex.org/I3020098449"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":0.6451,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.60740981,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"20","issue":"15","first_page":"1644","last_page":"1658"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12236","display_name":"Photoreceptor and optogenetics research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12236","display_name":"Photoreceptor and optogenetics research","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10077","display_name":"Neuroscience and Neuropharmacology Research","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9975000023841858,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/bacteriorhodopsin","display_name":"Bacteriorhodopsin","score":0.950211763381958},{"id":"https://openalex.org/keywords/isomerization","display_name":"Isomerization","score":0.719231903553009},{"id":"https://openalex.org/keywords/adiabatic-process","display_name":"Adiabatic process","score":0.6423890590667725},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5851162075996399},{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.5164918899536133},{"id":"https://openalex.org/keywords/potential-energy","display_name":"Potential energy","score":0.5129539370536804},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4261438846588135},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.41646867990493774},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.24242815375328064},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.23823124170303345},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.23004716634750366},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.22987863421440125},{"id":"https://openalex.org/keywords/atomic-physics","display_name":"Atomic physics","score":0.15211966633796692},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.13511642813682556}],"concepts":[{"id":"https://openalex.org/C189542057","wikidata":"https://www.wikidata.org/wiki/Q242310","display_name":"Bacteriorhodopsin","level":3,"score":0.950211763381958},{"id":"https://openalex.org/C126661725","wikidata":"https://www.wikidata.org/wiki/Q903420","display_name":"Isomerization","level":3,"score":0.719231903553009},{"id":"https://openalex.org/C109663097","wikidata":"https://www.wikidata.org/wiki/Q182453","display_name":"Adiabatic process","level":2,"score":0.6423890590667725},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5851162075996399},{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.5164918899536133},{"id":"https://openalex.org/C84551667","wikidata":"https://www.wikidata.org/wiki/Q155640","display_name":"Potential energy","level":2,"score":0.5129539370536804},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4261438846588135},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.41646867990493774},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.24242815375328064},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23823124170303345},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.23004716634750366},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.22987863421440125},{"id":"https://openalex.org/C184779094","wikidata":"https://www.wikidata.org/wiki/Q26383","display_name":"Atomic physics","level":1,"score":0.15211966633796692},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.13511642813682556},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.0},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":[],"locations_count":1,"locations":[{"id":"doi:10.1002/(sici)1096-987x(19991130)20:15<1644::aid-jcc5>3.0.co;2-y","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19991130)20:15<1644::aid-jcc5>3.0.co;2-y","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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":"Journal of Computational Chemistry","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.9200000166893005,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1968827114","https://openalex.org/W1976499671","https://openalex.org/W1977913371","https://openalex.org/W1978886142","https://openalex.org/W1989753444","https://openalex.org/W1991587990","https://openalex.org/W1991687440","https://openalex.org/W1996617034","https://openalex.org/W1997775954","https://openalex.org/W2002559842","https://openalex.org/W2005910905","https://openalex.org/W2009987871","https://openalex.org/W2027408247","https://openalex.org/W2040513229","https://openalex.org/W2058640536","https://openalex.org/W2062021082","https://openalex.org/W2062344290","https://openalex.org/W2064497637","https://openalex.org/W2070677982","https://openalex.org/W2073623394","https://openalex.org/W2084961110","https://openalex.org/W2103636724","https://openalex.org/W2106140689","https://openalex.org/W2112154906","https://openalex.org/W2162166182"],"related_works":["https://openalex.org/W810579573","https://openalex.org/W2067064272","https://openalex.org/W2013554156","https://openalex.org/W1964299829","https://openalex.org/W187980102","https://openalex.org/W4242400092","https://openalex.org/W1527994608","https://openalex.org/W1998214021","https://openalex.org/W1923702724","https://openalex.org/W2969805932"],"abstract_inverted_index":{"Accurate":[0],"calculation":[1],"of":[2,11,26,38,55,79,87,93,102,125],"potential":[3,57],"energy":[4,58,131],"and":[5,45,59,72,96,118],"free-energy":[6,60],"profiles":[7],"along":[8],"reaction":[9,81],"coordinates":[10,82],"biological":[12],"processes":[13],"such":[14],"as":[15],"enzymatic":[16],"reactions":[17],"or":[18],"conformational":[19],"changes":[20],"is":[21,104,133],"fundamental":[22],"to":[23,90,136],"the":[24,35,39,77,91,94,100,110,121,126],"obtention":[25],"theoretical":[27],"insight":[28],"into":[29],"protein":[30],"function.":[31],"We":[32],"describe":[33],"here":[34,135],"practical":[36],"implementation":[37],"Automatic":[40],"Map":[41],"Refinement":[42],"Procedure":[43],"(AMRP)":[44],"two-dimensional":[46],"Weighted":[47],"Histogram":[48],"Analysis":[49],"Method":[50],"(WHAM)":[51],"for":[52,64,73],"efficient":[53],"computation":[54],"adiabatic":[56],"maps,":[61],"respectively.":[62],"Methods":[63],"efficiently":[65],"sampling":[66],"configuration":[67],"space":[68],"with":[69,120],"high-energy":[70],"barriers":[71],"removing":[74],"hysteresis":[75],"in":[76,99,114],"case":[78],"periodic":[80],"are":[83],"presented.":[84],"The":[85],"application":[86],"these":[88],"techniques":[89],"isomerization":[92],"C13\uf8feC14":[95],"C15\uf8feN16":[97],"bonds":[98],"retinal":[101,111],"bacteriorhodopsin":[103,108],"described.":[105],"In":[106],"dark-adapted":[107],"(bR),":[109],"moiety":[112],"exists":[113],"two":[115],"conformers,":[116],"all-trans":[117],"(13,15)cis,":[119],"latter":[122],"making":[123],"\u224367%":[124],"population.":[127],"This":[128],"experimental":[129],"free":[130],"difference":[132],"reproduced":[134],"within":[137],"kBT.":[138],"\u00a91999":[139],"John":[140],"Wiley":[141],"&":[142],"Sons,":[143],"Inc.":[144],"J":[145],"Comput":[146],"Chem":[147],"20:":[148],"1644\u20131658,":[149],"1999":[150]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
