{"id":"https://openalex.org/W2060339536","doi":"https://doi.org/10.1002/(sici)1096-987x(19961115)17:14<1667::aid-jcc8>3.0.co;2-j","title":"A new method for side-chain conformation prediction using a Hopfield network and reproduced rotamers","display_name":"A new method for side-chain conformation prediction using a Hopfield network and reproduced rotamers","publication_year":1996,"publication_date":"1996-11-15","ids":{"openalex":"https://openalex.org/W2060339536","doi":"https://doi.org/10.1002/(sici)1096-987x(19961115)17:14<1667::aid-jcc8>3.0.co;2-j","mag":"2060339536"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1096-987x(19961115)17:14<1667::aid-jcc8>3.0.co;2-j","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19961115)17:14<1667::aid-jcc8>3.0.co;2-j","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/A5080123389","display_name":"Hidetoshi Kono","orcid":"https://orcid.org/0000-0001-5729-8707"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"HIDETOSHI KONO","raw_affiliation_strings":["Bioinformation Engineering Laboratory, Department of Biotechnology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113, Japan","Bioinformation Engineering Laboratory, Department of Biotechnology, The University of Tokyo, 1\u20101\u20101, Yayoi, Bunkyo\u2010ku, Tokyo 113, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformation Engineering Laboratory, Department of Biotechnology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Bioinformation Engineering Laboratory, Department of Biotechnology, The University of Tokyo, 1\u20101\u20101, Yayoi, Bunkyo\u2010ku, Tokyo 113, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010686893","display_name":"Junta Doi","orcid":null},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"JUNTA DOI","raw_affiliation_strings":["Bioinformation Engineering Laboratory, Department of Biotechnology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113, Japan","Bioinformation Engineering Laboratory, Department of Biotechnology, The University of Tokyo, 1\u20101\u20101, Yayoi, Bunkyo\u2010ku, Tokyo 113, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformation Engineering Laboratory, Department of Biotechnology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Bioinformation Engineering Laboratory, Department of Biotechnology, The University of Tokyo, 1\u20101\u20101, Yayoi, Bunkyo\u2010ku, Tokyo 113, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5010686893"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":0.5365,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.64233005,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"17","issue":"14","first_page":"1667","last_page":"1683"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9930999875068665,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9904999732971191,"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/conformational-isomerism","display_name":"Conformational isomerism","score":0.851057231426239},{"id":"https://openalex.org/keywords/side-chain","display_name":"Side chain","score":0.8474966287612915},{"id":"https://openalex.org/keywords/hydrogen-bond","display_name":"Hydrogen bond","score":0.6642859578132629},{"id":"https://openalex.org/keywords/energy-minimization","display_name":"Energy minimization","score":0.5441239476203918},{"id":"https://openalex.org/keywords/conformational-entropy","display_name":"Conformational entropy","score":0.5298903584480286},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4296831488609314},{"id":"https://openalex.org/keywords/chain","display_name":"Chain (unit)","score":0.4161009192466736},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3437645733356476},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3357682526111603},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3345491290092468},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.30355075001716614},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2515360116958618},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.19439542293548584},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.09402424097061157}],"concepts":[{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.851057231426239},{"id":"https://openalex.org/C204921945","wikidata":"https://www.wikidata.org/wiki/Q899689","display_name":"Side chain","level":3,"score":0.8474966287612915},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.6642859578132629},{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.5441239476203918},{"id":"https://openalex.org/C69308434","wikidata":"https://www.wikidata.org/wiki/Q5160266","display_name":"Conformational entropy","level":3,"score":0.5298903584480286},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4296831488609314},{"id":"https://openalex.org/C199185054","wikidata":"https://www.wikidata.org/wiki/Q552299","display_name":"Chain (unit)","level":2,"score":0.4161009192466736},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3437645733356476},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3357682526111603},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3345491290092468},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.30355075001716614},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2515360116958618},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.19439542293548584},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.09402424097061157},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/(sici)1096-987x(19961115)17:14<1667::aid-jcc8>3.0.co;2-j","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19961115)17:14<1667::aid-jcc8>3.0.co;2-j","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":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8899999856948853}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1498124562","https://openalex.org/W1574312817","https://openalex.org/W1597286183","https://openalex.org/W1966041739","https://openalex.org/W1970197953","https://openalex.org/W1971251199","https://openalex.org/W1971853518","https://openalex.org/W1972982314","https://openalex.org/W1975832522","https://openalex.org/W1979046104","https://openalex.org/W1987977716","https://openalex.org/W1992739911","https://openalex.org/W2008852962","https://openalex.org/W2027189612","https://openalex.org/W2034126246","https://openalex.org/W2036324972","https://openalex.org/W2037797286","https://openalex.org/W2050064341","https://openalex.org/W2051628563","https://openalex.org/W2063223774","https://openalex.org/W2070783701","https://openalex.org/W2088451388","https://openalex.org/W2138854816"],"related_works":["https://openalex.org/W2069758239","https://openalex.org/W2172114588","https://openalex.org/W2170971420","https://openalex.org/W2078482597","https://openalex.org/W2159625391","https://openalex.org/W2008852962","https://openalex.org/W2137170709","https://openalex.org/W2076138193","https://openalex.org/W2060339536","https://openalex.org/W2166317516"],"abstract_inverted_index":{"We":[0,40,162],"present":[1],"a":[2,12,42],"new":[3],"side-chain":[4,37,55,65,89,127,176,186],"prediction":[5],"method":[6,165],"based":[7],"on":[8,16],"energy":[9,155],"minimization":[10],"using":[11,192],"Hopfield":[13],"network,":[14],"focusing":[15],"the":[17,25,52,64,78,81,84,93,121,137,141,159,170,180,193],"buried":[18,104,131],"residues":[19,132],"of":[20,29,63,86,95,107,126,144],"proteins.":[21],"In":[22],"this":[23,164],"method,":[24],"network":[26],"is":[27],"composed":[28],"automata":[30],"assigned":[31],"to":[32,35,48,120,156,166,174],"each":[33],"rotamer":[34,43],"restrict":[36],"conformational":[38],"space.":[39],"reproduced":[41],"library":[44],"that":[45],"enabled":[46],"us":[47],"more":[49],"widely":[50],"cover":[51],"space":[53],"for":[54,103,130],"conformations":[56,177,187],"than":[57],"those":[58,191],"previously":[59],"produced.":[60],"The":[61,100,113,124],"accuracy":[62],"modeling":[66],"was":[67,110,115,133],"estimated":[68],"by":[69,198],"three":[70],"standards:":[71],"root":[72],"mean":[73],"square":[74],"deviations":[75],"(rmsds)":[76],"between":[77],"modeled":[79],"and":[80,92,183],"crystal":[82],"structures,":[83],"percentages":[85,94],"correctly":[87,96,145,189],"predicted":[88,97,146],"torsion":[90],"angles,":[91],"hydrogen":[98,138,147,153],"bonds.":[99],"average":[101,142],"rmsd":[102],"side":[105],"chains":[106],"21":[108],"proteins":[109],"1.10":[111],"\u00c5.":[112],"value":[114],"almost":[116],"always":[117],"improved":[118],"relative":[119],"previous":[122],"works.":[123],"percentage":[125,143],"X1":[128],"angles":[129],"87.3%.":[134],"By":[135],"considering":[136],"bond":[139,154,160],"energy,":[140],"bonds":[148],"rose":[149],"from":[150,179],"33%":[151],"without":[152],"52%":[157],"with":[158],"energy.":[161],"applied":[163],"homology":[167],"modeling,":[168],"where":[169],"protein":[171],"backbone":[172],"used":[173],"predict":[175,185],"deviates":[178],"correct":[181,194],"conformation,":[182],"could":[184],"as":[188,190],"backbones.":[195],"\u00a9":[196],"1996":[197],"John":[199],"Wiley":[200],"&":[201],"Sons,":[202],"Inc.":[203]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}