{"id":"https://openalex.org/W2116077517","doi":"https://doi.org/10.1002/(sici)1096-987x(19970430)18:6<723::aid-jcc1>3.0.co;2-u","title":"Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP?substrate complex","display_name":"Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP?substrate complex","publication_year":1997,"publication_date":"1997-04-30","ids":{"openalex":"https://openalex.org/W2116077517","doi":"https://doi.org/10.1002/(sici)1096-987x(19970430)18:6<723::aid-jcc1>3.0.co;2-u","mag":"2116077517"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1096-987x(19970430)18:6<723::aid-jcc1>3.0.co;2-u","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19970430)18:6<723::aid-jcc1>3.0.co;2-u","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/A5035048768","display_name":"Amedeo Caflisch","orcid":"https://orcid.org/0000-0002-2317-6792"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"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":["CH","US"],"is_corresponding":false,"raw_author_name":"Amedeo Caflisch","raw_affiliation_strings":["Biochemisches Institut der Universita\u0308t Zu\u0308rich, CH-8057 Zu\u0308rich, Switzerland","Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02140"],"affiliations":[{"raw_affiliation_string":"Biochemisches Institut der Universita\u0308t Zu\u0308rich, CH-8057 Zu\u0308rich, Switzerland","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02140","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028955075","display_name":"Stefan Fischer","orcid":"https://orcid.org/0000-0001-8811-7518"},"institutions":[{"id":"https://openalex.org/I4210128300","display_name":"Institut de Chimie","ror":"https://ror.org/02cte4b68","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4210128300"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210130154","display_name":"Laboratoire de Chimie","ror":"https://ror.org/02gaw1s20","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210130154"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"Stefan Fischer","raw_affiliation_strings":["Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02140","Laboratoire de Chimie Biophysique, Institut Le Bel, Universite\u0301 Louis Pasteur, F-6700 Strasbourg, France"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02140","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Laboratoire de Chimie Biophysique, Institut Le Bel, Universite\u0301 Louis Pasteur, F-6700 Strasbourg, France","institution_ids":["https://openalex.org/I4210128300","https://openalex.org/I4210130154"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076499540","display_name":"Martin Karplus","orcid":"https://orcid.org/0000-0002-5485-6117"},"institutions":[{"id":"https://openalex.org/I4210128300","display_name":"Institut de Chimie","ror":"https://ror.org/02cte4b68","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4210128300"]},{"id":"https://openalex.org/I4210130154","display_name":"Laboratoire de Chimie","ror":"https://ror.org/02gaw1s20","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I113428412","https://openalex.org/I1294671590","https://openalex.org/I203339264","https://openalex.org/I203339264","https://openalex.org/I4210130154"]},{"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":["FR","US"],"is_corresponding":true,"raw_author_name":"Martin Karplus","raw_affiliation_strings":["Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02140","Laboratoire de Chimie Biophysique, Institut Le Bel, Universite\u0301 Louis Pasteur, F-6700 Strasbourg, France"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02140","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Laboratoire de Chimie Biophysique, Institut Le Bel, Universite\u0301 Louis Pasteur, F-6700 Strasbourg, France","institution_ids":["https://openalex.org/I4210128300","https://openalex.org/I4210130154"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5076499540"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210128300","https://openalex.org/I4210130154"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":2.0895,"has_fulltext":false,"cited_by_count":60,"citation_normalized_percentile":{"value":0.87975086,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"18","issue":"6","first_page":"723","last_page":"743"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12620","display_name":"Signaling Pathways in Disease","score":0.9997000098228455,"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/T12620","display_name":"Signaling Pathways in Disease","score":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9232000112533569,"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9031999707221985,"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/tetrapeptide","display_name":"Tetrapeptide","score":0.8064407110214233},{"id":"https://openalex.org/keywords/fkbp","display_name":"FKBP","score":0.780551552772522},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.7352645993232727},{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.719232439994812},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5730903148651123},{"id":"https://openalex.org/keywords/implicit-solvation","display_name":"Implicit solvation","score":0.5073117613792419},{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.5039052367210388},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.49253496527671814},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.4606130123138428},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.44960668683052063},{"id":"https://openalex.org/keywords/binding-energy","display_name":"Binding energy","score":0.43033719062805176},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3387896716594696},{"id":"https://openalex.org/keywords/solvent","display_name":"Solvent","score":0.30106738209724426},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.1442028284072876},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.0930696427822113},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08657845854759216},{"id":"https://openalex.org/keywords/atomic-physics","display_name":"Atomic physics","score":0.07972928881645203},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.0670691728591919}],"concepts":[{"id":"https://openalex.org/C2779564779","wikidata":"https://www.wikidata.org/wiki/Q7706647","display_name":"Tetrapeptide","level":3,"score":0.8064407110214233},{"id":"https://openalex.org/C133956753","wikidata":"https://www.wikidata.org/wiki/Q583864","display_name":"FKBP","level":2,"score":0.780551552772522},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7352645993232727},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.719232439994812},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5730903148651123},{"id":"https://openalex.org/C64147673","wikidata":"https://www.wikidata.org/wiki/Q6007318","display_name":"Implicit solvation","level":4,"score":0.5073117613792419},{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.5039052367210388},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.49253496527671814},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.4606130123138428},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.44960668683052063},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.43033719062805176},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3387896716594696},{"id":"https://openalex.org/C2780471494","wikidata":"https://www.wikidata.org/wiki/Q146505","display_name":"Solvent","level":2,"score":0.30106738209724426},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.1442028284072876},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0930696427822113},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08657845854759216},{"id":"https://openalex.org/C184779094","wikidata":"https://www.wikidata.org/wiki/Q26383","display_name":"Atomic physics","level":1,"score":0.07972928881645203},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.0670691728591919},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"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/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1002/(sici)1096-987x(19970430)18:6<723::aid-jcc1>3.0.co;2-u","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19970430)18:6<723::aid-jcc1>3.0.co;2-u","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"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.94.9466","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.94.9466","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.biochem-caflisch.uzh.ch/Caflisch/compchem1997.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.5799999833106995,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W33851185","https://openalex.org/W1497188274","https://openalex.org/W1526056362","https://openalex.org/W1563633234","https://openalex.org/W1969971113","https://openalex.org/W1976129849","https://openalex.org/W1978084071","https://openalex.org/W1978879981","https://openalex.org/W1980028982","https://openalex.org/W1982283652","https://openalex.org/W1989488118","https://openalex.org/W1990664560","https://openalex.org/W1996929472","https://openalex.org/W1997639796","https://openalex.org/W1998208404","https://openalex.org/W1999347494","https://openalex.org/W1999724806","https://openalex.org/W1999968212","https://openalex.org/W2003800442","https://openalex.org/W2012231377","https://openalex.org/W2013785414","https://openalex.org/W2017639307","https://openalex.org/W2019386320","https://openalex.org/W2020002894","https://openalex.org/W2023940675","https://openalex.org/W2024842574","https://openalex.org/W2026398915","https://openalex.org/W2028231353","https://openalex.org/W2032518125","https://openalex.org/W2039519959","https://openalex.org/W2039665613","https://openalex.org/W2040830056","https://openalex.org/W2042446618","https://openalex.org/W2047174875","https://openalex.org/W2047730466","https://openalex.org/W2048682054","https://openalex.org/W2052741482","https://openalex.org/W2053289371","https://openalex.org/W2056760934","https://openalex.org/W2060100446","https://openalex.org/W2062129975","https://openalex.org/W2064407644","https://openalex.org/W2071023459","https://openalex.org/W2071911426","https://openalex.org/W2075662564","https://openalex.org/W2077140822","https://openalex.org/W2078277930","https://openalex.org/W2094779443","https://openalex.org/W2110043143","https://openalex.org/W2110774526","https://openalex.org/W2116712176","https://openalex.org/W2141509259","https://openalex.org/W2142713587","https://openalex.org/W2156160283","https://openalex.org/W2162166182","https://openalex.org/W2316564661","https://openalex.org/W3141421247","https://openalex.org/W4247951394"],"related_works":["https://openalex.org/W1966793603","https://openalex.org/W2048341727","https://openalex.org/W2089507369","https://openalex.org/W2045242973","https://openalex.org/W1974433778","https://openalex.org/W2498829061","https://openalex.org/W2053689559","https://openalex.org/W4323037679","https://openalex.org/W2322826137","https://openalex.org/W2105465678"],"abstract_inverted_index":{"A":[0],"Monte":[1,91],"Carlo":[2,92],"docking":[3,60],"procedure":[4],"that":[5],"combines":[6],"random":[7],"displacements":[8],"of":[9,18,31,46,66,84,101,135,145,172,219,225,234,262,291,318,338,341,349,358,365],"the":[10,19,28,32,37,47,52,59,67,90,96,102,125,133,136,142,152,156,170,173,177,181,206,220,226,235,248,253,259,263,279,286,301,315,323,336,339,355,363],"substrate":[11,68,249,273],"and":[12,24,51,111,155,299,361],"protein":[13,40],"side":[14,217],"chains":[15,199,218],"with":[16,165,176,191,215,285,314],"minimization":[17],"enzyme\u2014substrate":[20,174],"complex":[21,175,250,281],"is":[22,69,115,149,163,183,210,282,312],"described":[23,328],"applied":[25],"to":[26,36,79,132,195,200,297],"finding":[27],"binding":[29,39,54,86,98,222,241],"mode":[30],"blocked":[33],"tetrapeptide":[34,182,236],"N-acetyl-Leu-Pro-Phe-methylamide":[35],"FK506":[38],"(FKBP).":[41],"The":[42,62,73,239,275,326],"tetrapeptide,":[43],"an":[44,269],"analog":[45],"preferred":[48],"FKBP":[49,53,221,240,298,319],"substrate,":[50],"site":[55,87,242],"are":[56,76,121,139,237],"flexible":[57],"during":[58,71,89],"procedure.":[61],"twisted-imide":[63],"transition-state":[64],"form":[65],"used":[70],"docking.":[72],"enzyme":[74,324],"charges":[75],"scaled":[77],"individually":[78],"account":[80],"for":[81,108,205,258,278,335,354,362],"solvent":[82,192,366],"screening":[83],"specific":[85],"residues":[88],"sampling.":[93],"To":[94],"evaluate":[95],"relative":[97],"free":[99,143,179],"energies":[100,120],"resulting":[103],"structures,":[104],"a":[105,166,186,244,292,342,350],"rapid":[106],"method":[107],"calculating":[109],"polar":[110,213],"nonpolar":[112,130],"solvation":[113],"effects":[114,317],"introduced.":[116],"Accurate":[117],"electrostatic":[118],"solute\u2014solvent":[119,157],"calculated":[122,164],"by":[123,141,305,370],"solving":[124],"finite-difference":[126],"linearized":[127],"Poisson\u2014Boltzmann":[128],"equation;":[129],"contributions":[131],"stability":[134],"different":[137],"conformers":[138],"estimated":[140],"energy":[144],"cavity":[146],"formation,":[147],"which":[148,162,209,267],"obtained":[150,303],"from":[151],"molecular":[153],"surface,":[154],"van":[158],"der":[159],"Waals":[160],"energy,":[161,180],"continuum":[167],"approach.":[168],"In":[169,309],"conformation":[171,246],"lowest":[178],"bound":[184,296],"as":[185,202,251,347],"type":[187],"VIa":[188],"proline":[189],"turn":[190],"accessible":[193],"ends":[194],"permit":[196],"longer":[197],"polypeptide":[198],"act":[201],"substrates.":[203],"Except":[204],"imide":[207],"carbonyl,":[208],"involved":[211],"in":[212,247,252,272,283,333,344],"interactions":[214],"aromatic":[216],"site,":[223],"all":[224],"seven":[227],"potential":[228],"hydrogen":[229],"bond":[230],"donors":[231],"or":[232,346],"acceptors":[233],"satisfied.":[238],"has":[243],"similar":[245],"FKBP-FK506":[254],"cocrystal":[255],"structure,":[256],"except":[257],"predicted":[260],"reorientation":[261],"Tyr":[264],"82":[265],"hydroxyl,":[266],"plays":[268],"important":[270],"role":[271],"binding.":[274],"present":[276],"model":[277,307],"FKBP\u2014substrate":[280],"agreement":[284],"recently":[287],"determined":[288],"crystal":[289],"structure":[290,302,340],"cyclic":[293],"peptide\u2014FK506":[294],"hybrid":[295],"supports":[300],"previously":[304],"iterative":[306],"building.":[308],"addition,":[310],"it":[311],"consistent":[313],"observed":[316],"point":[320],"mutations":[321],"on":[322],"activity.":[325],"approach":[327],"here":[329],"should":[330],"be":[331],"useful,":[332],"general,":[334],"prediction":[337],"molecule":[343],"solution":[345],"part":[348],"complex.":[351],"It":[352],"provides":[353],"effective":[356],"sampling":[357],"conformational":[359],"space":[360],"inclusion":[364],"effects.":[367],"\u00a9":[368],"1997":[369],"John":[371],"Wiley":[372],"&":[373],"Sons,":[374],"Inc.":[375]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}