{"id":"https://openalex.org/W2124477618","doi":"https://doi.org/10.1002/(sici)1096-987x(199603)17:4<476::aid-jcc8>3.0.co;2-r","title":"New implementation of and the modeling by the extended simulated annealing process to structures of T4 lysozyme mutants at the 86th residue","display_name":"New implementation of and the modeling by the extended simulated annealing process to structures of T4 lysozyme mutants at the 86th residue","publication_year":1996,"publication_date":"1996-03-01","ids":{"openalex":"https://openalex.org/W2124477618","doi":"https://doi.org/10.1002/(sici)1096-987x(199603)17:4<476::aid-jcc8>3.0.co;2-r","mag":"2124477618"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1096-987x(199603)17:4<476::aid-jcc8>3.0.co;2-r","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(199603)17:4<476::aid-jcc8>3.0.co;2-r","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/A5103256544","display_name":"Shigeru Endo","orcid":"https://orcid.org/0000-0002-1899-6358"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Shigeru Endo","raw_affiliation_strings":["Protein Array Project, ERATO, JRDC, 5-9-1, Tokodai, Tsukuba 300-26, Japan","Protein Array Project, ERATO, JRDC, 5\u20109\u20101, Tokodai, Tsukuba 300\u201026, Japan"],"affiliations":[{"raw_affiliation_string":"Protein Array Project, ERATO, JRDC, 5-9-1, Tokodai, Tsukuba 300-26, Japan","institution_ids":[]},{"raw_affiliation_string":"Protein Array Project, ERATO, JRDC, 5\u20109\u20101, Tokodai, Tsukuba 300\u201026, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056979882","display_name":"Junichi Higo","orcid":"https://orcid.org/0000-0002-0408-1907"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Junichi Higo","raw_affiliation_strings":["Protein Array Project, ERATO, JRDC, 5-9-1, Tokodai, Tsukuba 300-26, Japan","Protein Array Project, ERATO, JRDC, 5\u20109\u20101, Tokodai, Tsukuba 300\u201026, Japan"],"affiliations":[{"raw_affiliation_string":"Protein Array Project, ERATO, JRDC, 5-9-1, Tokodai, Tsukuba 300-26, Japan","institution_ids":[]},{"raw_affiliation_string":"Protein Array Project, ERATO, JRDC, 5\u20109\u20101, Tokodai, Tsukuba 300\u201026, Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035756447","display_name":"Kuniaki Nagayama","orcid":"https://orcid.org/0000-0002-8092-3360"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kuniaki Nagayama","raw_affiliation_strings":["Protein Array Project, ERATO, JRDC, 5-9-1, Tokodai, Tsukuba 300-26, Japan","Protein Array Project, ERATO, JRDC, 5\u20109\u20101, Tokodai, Tsukuba 300\u201026, Japan"],"affiliations":[{"raw_affiliation_string":"Protein Array Project, ERATO, JRDC, 5-9-1, Tokodai, Tsukuba 300-26, Japan","institution_ids":[]},{"raw_affiliation_string":"Protein Array Project, ERATO, JRDC, 5\u20109\u20101, Tokodai, Tsukuba 300\u201026, Japan","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045201764","display_name":"Hiroshi Wako","orcid":"https://orcid.org/0000-0002-8265-1223"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroshi Wako","raw_affiliation_strings":["School of Social Sciences, Waseda University, Nishi-Waseda, Shinjuku-ku, Tokyo 169-50, Japan","School of Social Sciences, Waseda University, Nishi\u2010Waseda, Shinjuku\u2010ku, Tokyo 169\u201050, Japan"],"affiliations":[{"raw_affiliation_string":"School of Social Sciences, Waseda University, Nishi-Waseda, Shinjuku-ku, Tokyo 169-50, Japan","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"School of Social Sciences, Waseda University, Nishi\u2010Waseda, Shinjuku\u2010ku, Tokyo 169\u201050, Japan","institution_ids":["https://openalex.org/I150744194"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5103256544"],"corresponding_institution_ids":[],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":0.9971,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.76178842,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"4","first_page":"476","last_page":"488"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9943000078201294,"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/chemistry","display_name":"Chemistry","score":0.673966646194458},{"id":"https://openalex.org/keywords/lysozyme","display_name":"Lysozyme","score":0.6094590425491333},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.5946827530860901},{"id":"https://openalex.org/keywords/van-der-waals-force","display_name":"van der Waals force","score":0.5372706651687622},{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.5232738256454468},{"id":"https://openalex.org/keywords/annealing","display_name":"Annealing (glass)","score":0.5018255710601807},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.4955390691757202},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.492021769285202},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.4855956435203552},{"id":"https://openalex.org/keywords/simulated-annealing","display_name":"Simulated annealing","score":0.4768470525741577},{"id":"https://openalex.org/keywords/macromolecule","display_name":"Macromolecule","score":0.47110679745674133},{"id":"https://openalex.org/keywords/molecular-model","display_name":"Molecular model","score":0.4590770900249481},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.43459251523017883},{"id":"https://openalex.org/keywords/maxima-and-minima","display_name":"Maxima and minima","score":0.4136577844619751},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.36155033111572266},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.3331291675567627},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1852717101573944},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.16916677355766296},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12479209899902344},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11618191003799438},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.08208084106445312}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.673966646194458},{"id":"https://openalex.org/C2776966407","wikidata":"https://www.wikidata.org/wiki/Q24779410","display_name":"Lysozyme","level":2,"score":0.6094590425491333},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.5946827530860901},{"id":"https://openalex.org/C126061179","wikidata":"https://www.wikidata.org/wiki/Q189627","display_name":"van der Waals force","level":3,"score":0.5372706651687622},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.5232738256454468},{"id":"https://openalex.org/C2777855556","wikidata":"https://www.wikidata.org/wiki/Q4339544","display_name":"Annealing (glass)","level":2,"score":0.5018255710601807},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.4955390691757202},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.492021769285202},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.4855956435203552},{"id":"https://openalex.org/C126980161","wikidata":"https://www.wikidata.org/wiki/Q863783","display_name":"Simulated annealing","level":2,"score":0.4768470525741577},{"id":"https://openalex.org/C204389451","wikidata":"https://www.wikidata.org/wiki/Q178593","display_name":"Macromolecule","level":2,"score":0.47110679745674133},{"id":"https://openalex.org/C178910836","wikidata":"https://www.wikidata.org/wiki/Q2196961","display_name":"Molecular model","level":2,"score":0.4590770900249481},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.43459251523017883},{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.4136577844619751},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.36155033111572266},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.3331291675567627},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1852717101573944},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.16916677355766296},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12479209899902344},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11618191003799438},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.08208084106445312},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/(sici)1096-987x(199603)17:4<476::aid-jcc8>3.0.co;2-r","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(199603)17:4<476::aid-jcc8>3.0.co;2-r","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":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1572000980","https://openalex.org/W1590020374","https://openalex.org/W1966041739","https://openalex.org/W1971622334","https://openalex.org/W1975420352","https://openalex.org/W1977911529","https://openalex.org/W1987229563","https://openalex.org/W1987977716","https://openalex.org/W2000908837","https://openalex.org/W2001130582","https://openalex.org/W2001304403","https://openalex.org/W2017788188","https://openalex.org/W2025947203","https://openalex.org/W2029733983","https://openalex.org/W2030470356","https://openalex.org/W2042501418","https://openalex.org/W2056760934","https://openalex.org/W2061346531","https://openalex.org/W2064819913","https://openalex.org/W2069454751","https://openalex.org/W2079589162","https://openalex.org/W2089463116","https://openalex.org/W2091477689","https://openalex.org/W2103714936","https://openalex.org/W2113247058","https://openalex.org/W2118087331","https://openalex.org/W2139259254","https://openalex.org/W2149315921","https://openalex.org/W4230223507"],"related_works":["https://openalex.org/W2914878125","https://openalex.org/W1913424772","https://openalex.org/W2368942211","https://openalex.org/W2001717794","https://openalex.org/W2314385229","https://openalex.org/W1541765418","https://openalex.org/W2067924147","https://openalex.org/W2441126129","https://openalex.org/W2132461435","https://openalex.org/W1992534732"],"abstract_inverted_index":{"The":[0,139],"extended":[1],"simulated":[2],"annealing":[3],"process":[4],"(ESAP)":[5],"is":[6,30,51,91],"a":[7,27,129,195],"useful":[8],"method":[9],"for":[10,47,105,154,162,175],"modeling":[11,106],"the":[12,39,44,49,55,60,76,118,136,146,163,169,177],"partial":[13,41],"structure":[14,50,131,148,170,179],"of":[15,62,113,171],"proteins":[16],"[J.":[17],"Higo":[18],"et":[19],"al.,":[20],"Biopolymers,":[21],"32,":[22],"33":[23],"(1992)].":[24],"In":[25],"ESAP,":[26],"protein":[28],"molecule":[29],"divided":[31],"into":[32,97],"two":[33],"parts:":[34],"small,":[35],"flexible":[36],"fragments":[37],"constituting":[38],"concerned":[40],"structure,":[42],"and":[43,158],"remaining":[45],"part,":[46],"which":[48,176],"kept":[52],"rigid":[53,77],"during":[54],"simulation.":[56],"We":[57,166],"have":[58],"improved":[59,101],"program":[61,102],"ESAP":[63,185],"so":[64],"that":[65,132],"it":[66],"can":[67,79,186],"be":[68,80,187],"adapted":[69],"to":[70,82,93,135,151,189,194],"general":[71],"macromolecules.":[72],"Any":[73],"sidechain":[74],"on":[75],"part":[78],"set":[81],"rotate.":[83],"Soft":[84],"repulsion":[85],"between":[86],"van":[87],"der":[88],"Waals":[89],"spheres":[90],"introduced":[92],"avoid":[94],"conformational":[95],"trapping":[96],"local":[98],"minima.":[99],"This":[100],"was":[103,133],"tested":[104],"structural":[107,191],"changes":[108,192],"caused":[109],"by":[110,203],"eight":[111],"kinds":[112],"amino":[114],"acid":[115],"mutation":[116,198],"at":[117],"86th":[119],"residue":[120,197],"in":[121,199],"T4":[122],"lysozyme.":[123],"For":[124],"each":[125],"mutant":[126],"we":[127],"obtained":[128],"model":[130,190],"close":[134],"X-ray":[137,147,178],"structure.":[138],"root":[140],"mean":[141],"square":[142],"(rms)":[143],"deviations":[144],"from":[145],"were":[149],"0.3":[150],"0.8":[152],"\u00c5":[153,161],"all":[155],"heavy":[156],"atoms":[157],"about":[159],"0.2":[160],"main-chain":[164],"atoms.":[165],"also":[167],"modeled":[168],"an":[172],"Ile":[173],"mutant,":[174],"has":[180],"not":[181],"yet":[182],"been":[183],"reported.":[184],"used":[188],"due":[193],"single":[196],"proteins.":[200],"\u00a9":[201],"1996":[202],"John":[204],"Wiley":[205],"&":[206],"Sons,":[207],"Inc.":[208]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}