{"id":"https://openalex.org/W2087542675","doi":"https://doi.org/10.1002/jcc.540151210","title":"A rapid and efficient algorithm for packing polypeptide chains by energy minimization","display_name":"A rapid and efficient algorithm for packing polypeptide chains by energy minimization","publication_year":1994,"publication_date":"1994-12-01","ids":{"openalex":"https://openalex.org/W2087542675","doi":"https://doi.org/10.1002/jcc.540151210","mag":"2087542675"},"language":"en","primary_location":{"id":"doi:10.1002/jcc.540151210","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.540151210","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/A5113637923","display_name":"Kenneth D. Gibson","orcid":null},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kenneth D. Gibson","raw_affiliation_strings":["Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301","Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853\u20131301"],"affiliations":[{"raw_affiliation_string":"Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853\u20131301","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022665888","display_name":"Harold A. Scheraga","orcid":"https://orcid.org/0000-0002-6314-5376"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Harold A. Scheraga","raw_affiliation_strings":["Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301","Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853\u20131301"],"affiliations":[{"raw_affiliation_string":"Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853\u20131301","institution_ids":["https://openalex.org/I205783295"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5022665888"],"corresponding_institution_ids":["https://openalex.org/I205783295"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":0.9468,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.75088381,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"15","issue":"12","first_page":"1403","last_page":"1413"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12085","display_name":"Collagen: Extraction and Characterization","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/2502","display_name":"Biomaterials"},"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/T12085","display_name":"Collagen: Extraction and Characterization","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/2502","display_name":"Biomaterials"},"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/T11966","display_name":"Silk-based biomaterials and applications","score":0.9901000261306763,"subfield":{"id":"https://openalex.org/subfields/2502","display_name":"Biomaterials"},"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/T10831","display_name":"Cell Adhesion Molecules Research","score":0.9883000254631042,"subfield":{"id":"https://openalex.org/subfields/2723","display_name":"Immunology and Allergy"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/antiparallel","display_name":"Antiparallel (mathematics)","score":0.824860155582428},{"id":"https://openalex.org/keywords/energy-minimization","display_name":"Energy minimization","score":0.7500556707382202},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6957675814628601},{"id":"https://openalex.org/keywords/minification","display_name":"Minification","score":0.6641362309455872},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6458138823509216},{"id":"https://openalex.org/keywords/convergence","display_name":"Convergence (economics)","score":0.6143214702606201},{"id":"https://openalex.org/keywords/chain","display_name":"Chain (unit)","score":0.4662196934223175},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.454950749874115},{"id":"https://openalex.org/keywords/side-chain","display_name":"Side chain","score":0.4112032353878021},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4070962965488434},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.3958074748516083},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3896830677986145},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3793765902519226},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.36903923749923706},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.3660925030708313},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.3349951207637787},{"id":"https://openalex.org/keywords/polymer","display_name":"Polymer","score":0.2576729655265808},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.23503124713897705},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.214575856924057},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.21341916918754578},{"id":"https://openalex.org/keywords/composite-material","display_name":"Composite material","score":0.10435342788696289}],"concepts":[{"id":"https://openalex.org/C142089489","wikidata":"https://www.wikidata.org/wiki/Q1053976","display_name":"Antiparallel (mathematics)","level":3,"score":0.824860155582428},{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.7500556707382202},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6957675814628601},{"id":"https://openalex.org/C147764199","wikidata":"https://www.wikidata.org/wiki/Q6865248","display_name":"Minification","level":2,"score":0.6641362309455872},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6458138823509216},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.6143214702606201},{"id":"https://openalex.org/C199185054","wikidata":"https://www.wikidata.org/wiki/Q552299","display_name":"Chain (unit)","level":2,"score":0.4662196934223175},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.454950749874115},{"id":"https://openalex.org/C204921945","wikidata":"https://www.wikidata.org/wiki/Q899689","display_name":"Side chain","level":3,"score":0.4112032353878021},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4070962965488434},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.3958074748516083},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3896830677986145},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3793765902519226},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.36903923749923706},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3660925030708313},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.3349951207637787},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.2576729655265808},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23503124713897705},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.214575856924057},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.21341916918754578},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.10435342788696289},{"id":"https://openalex.org/C50522688","wikidata":"https://www.wikidata.org/wiki/Q189833","display_name":"Economic growth","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C115260700","wikidata":"https://www.wikidata.org/wiki/Q11408","display_name":"Magnetic field","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/jcc.540151210","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.540151210","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","score":0.9100000262260437,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W39947340","https://openalex.org/W1537715248","https://openalex.org/W1600524405","https://openalex.org/W1965433785","https://openalex.org/W1973229646","https://openalex.org/W1974197103","https://openalex.org/W1976308311","https://openalex.org/W1982831035","https://openalex.org/W1991078253","https://openalex.org/W1999612183","https://openalex.org/W2001130582","https://openalex.org/W2006874604","https://openalex.org/W2009272934","https://openalex.org/W2012005320","https://openalex.org/W2027063058","https://openalex.org/W2030935884","https://openalex.org/W2034010568","https://openalex.org/W2055413087","https://openalex.org/W2060503194","https://openalex.org/W2062081085","https://openalex.org/W2065876439","https://openalex.org/W2067228077","https://openalex.org/W2067773244","https://openalex.org/W2073229964","https://openalex.org/W2074339198","https://openalex.org/W2078484296","https://openalex.org/W2078899806","https://openalex.org/W2078948837","https://openalex.org/W2079589162","https://openalex.org/W2086902963","https://openalex.org/W2089463116","https://openalex.org/W2091418430","https://openalex.org/W2107763310","https://openalex.org/W2124660391","https://openalex.org/W2138132608","https://openalex.org/W2140489469","https://openalex.org/W2143883886","https://openalex.org/W2152255924","https://openalex.org/W2158528894","https://openalex.org/W2796985193","https://openalex.org/W2997715027"],"related_works":["https://openalex.org/W1518796764","https://openalex.org/W347294048","https://openalex.org/W2118841422","https://openalex.org/W2226908759","https://openalex.org/W1981231660","https://openalex.org/W2110536527","https://openalex.org/W2351116219","https://openalex.org/W1483822002","https://openalex.org/W2061881449","https://openalex.org/W2121257894"],"abstract_inverted_index":{"Abstract":[0],"An":[1],"improved":[2],"algorithm":[3,30,72],"for":[4,38,60],"packing":[5],"polypeptide":[6,44,69],"chains":[7],"with":[8,163],"fixed":[9],"geometry,":[10],"which":[11],"converges":[12],"to":[13,33,76,123,137],"a":[14],"local":[15],"energy":[16,63,79,158],"minimum":[17],"rapidly":[18],"and":[19,46,93,110,126,145,149],"efficiently,":[20],"is":[21,31,48],"described.":[22],"The":[23,71,140],"speed":[24,54],"of":[25,27,35,42,55,57,64,67,80,106,127],"convergence":[26,56],"the":[28,40,53,62,78,107,128,150,168],"new":[29],"comparable":[32],"that":[34],"existing":[36],"algorithms":[37,59],"minimizing":[39,61],"energies":[41],"single":[43],"chains,":[45],"it":[47],"several":[49,68],"times":[50],"greater":[51],"than":[52],"previous":[58],"structures":[65,103,118,135,170],"consisting":[66],"chains.":[70],"has":[73],"been":[74],"used":[75,119,136],"minimize":[77],"three\u2010stranded":[81,87,108],"(":[82,88,95,131],"L":[83,89,96,113,115,132,142],"\u2010Ala)":[84],"8":[85],"\u03b2\u2010sheets,":[86,92,99],"\u2010Val)":[90],"6":[91,98,134],"five\u2010stranded":[94],"\u2010Ile)":[97],"starting":[100],"from":[101,165],"regular":[102,109,156],"found":[104],"previously;":[105],"truncated":[111],"(Gly\u2010":[112],"\u2010Pro\u2010":[114],"\u2010Pro)":[116],"4":[117],"in":[120],"earlier":[121,166],"work":[122],"model":[124,138],"collagen;":[125],"stacked":[129],"\u03b2\u2010sheet":[130],"\u2010Ala\u2010GLy)":[133],"silk.":[139],"antiparallel":[141],"\u2010Ala":[143],"\u03b2\u2010sheet,":[144],"Gly\u2010Pro\u2010Pro":[146],"triple":[147],"helices,":[148],"silk":[151],"II":[152],"structure":[153],"remained":[154],"nearly":[155],"after":[157],"minimization,":[159],"but":[160],"by":[161,176],"contrast":[162],"results":[164],"computations":[167],"other":[169],"became":[171],"significantly":[172],"irregular.":[173],"\u00a9":[174],"1994":[175],"John":[177],"Wiley":[178],"&amp;":[179],"Sons,":[180],"Inc.":[181]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
