{"id":"https://openalex.org/W2001277732","doi":"https://doi.org/10.1002/jcc.540151006","title":"Efficient parallelization of the energy, surface, and derivative calculations for internal coordinate mechanics","display_name":"Efficient parallelization of the energy, surface, and derivative calculations for internal coordinate mechanics","publication_year":1994,"publication_date":"1994-10-01","ids":{"openalex":"https://openalex.org/W2001277732","doi":"https://doi.org/10.1002/jcc.540151006","mag":"2001277732"},"language":"en","primary_location":{"id":"doi:10.1002/jcc.540151006","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.540151006","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/A5070322806","display_name":"Maxim Totrov","orcid":"https://orcid.org/0000-0001-8594-274X"},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Maxim Totrov","raw_affiliation_strings":["European Molecular Biology Laboratory, Postfach 102209, Meyerhofstrasse, 1, 69012, Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, Postfach 102209, Meyerhofstrasse, 1, 69012, Heidelberg, Germany","institution_ids":["https://openalex.org/I4210153543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064101943","display_name":"Ruben Abagyan","orcid":"https://orcid.org/0000-0001-9309-2976"},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ruben Abagyan","raw_affiliation_strings":["European Molecular Biology Laboratory, Postfach 102209, Meyerhofstrasse, 1, 69012, Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory, Postfach 102209, Meyerhofstrasse, 1, 69012, Heidelberg, Germany","institution_ids":["https://openalex.org/I4210153543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5064101943"],"corresponding_institution_ids":["https://openalex.org/I4210153543"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":0.4039,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.55365119,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"15","issue":"10","first_page":"1105","last_page":"1112"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9990000128746033,"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":0.9990000128746033,"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":0.995199978351593,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.9884999990463257,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.7624962329864502},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"Dihedral angle","score":0.656663179397583},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5601032376289368},{"id":"https://openalex.org/keywords/internal-energy","display_name":"Internal energy","score":0.5242139101028442},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.44321373105049133},{"id":"https://openalex.org/keywords/coordinate-space","display_name":"Coordinate space","score":0.4322258234024048},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.41857945919036865},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.30785486102104187},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2158045768737793},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1955430805683136},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.11613267660140991},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.11575233936309814}],"concepts":[{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.7624962329864502},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.656663179397583},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5601032376289368},{"id":"https://openalex.org/C65494353","wikidata":"https://www.wikidata.org/wiki/Q180241","display_name":"Internal energy","level":2,"score":0.5242139101028442},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.44321373105049133},{"id":"https://openalex.org/C162291796","wikidata":"https://www.wikidata.org/wiki/Q125977","display_name":"Coordinate space","level":2,"score":0.4322258234024048},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.41857945919036865},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.30785486102104187},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2158045768737793},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1955430805683136},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.11613267660140991},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.11575233936309814},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.0},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/jcc.540151006","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.540151006","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":0.9100000262260437}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1584189892","https://openalex.org/W1966041739","https://openalex.org/W1973671260","https://openalex.org/W1980737536","https://openalex.org/W2001900040","https://openalex.org/W2005651680","https://openalex.org/W2013785414","https://openalex.org/W2014570683","https://openalex.org/W2017164460","https://openalex.org/W2027638447","https://openalex.org/W2029087609","https://openalex.org/W2034126246","https://openalex.org/W2061346531","https://openalex.org/W2062256089","https://openalex.org/W2064232089","https://openalex.org/W2070161012","https://openalex.org/W2073082810","https://openalex.org/W2074763159","https://openalex.org/W2079589162","https://openalex.org/W2102346174","https://openalex.org/W2121240117","https://openalex.org/W2139259254","https://openalex.org/W2145778955","https://openalex.org/W2149489299"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2128884622","https://openalex.org/W2112380088","https://openalex.org/W1715467939","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2027972911","https://openalex.org/W2146343568","https://openalex.org/W2013643406"],"abstract_inverted_index":{"Abstract":[0],"An":[1],"efficient":[2],"algorithm":[3],"for":[4,77,96,111],"parallelization":[5],"of":[6,15,66,103,109],"a":[7,90,97,104,107],"molecular":[8],"mechanics":[9],"program":[10,91],"operating":[11],"in":[12,89],"the":[13,40,78,101],"space":[14],"internal":[16,41],"coordinates":[17,42],"such":[18],"as":[19],"dihedral":[20],"angles,":[21,23],"bond":[22,25],"and":[24,54,62,85],"lengths":[26],"is":[27,82],"described.":[28],"The":[29,74,93],"iterative":[30],"procedure":[31],"to":[32,39,45],"calculate":[33,52],"analytical":[34],"energy":[35,53,61,102],"derivatives":[36],"with":[37,70],"respect":[38],"was":[43],"modified":[44],"allow":[46],"parallelization.":[47],"Computationally":[48],"intensive":[49],"modules":[50],"that":[51,63],"its":[55],"derivatives,":[56],"solvent\u2010accessible":[57],"surface,":[58],"electrostatic":[59],"polarization":[60],"update":[64],"lists":[65],"interactions":[67],"were":[68],"parallelized":[69],"nearly":[71],"100%":[72],"efficiency.":[73],"proposed":[75],"strategy":[76],"shared\u2010memory":[79],"computer":[80],"architecture":[81],"easily":[83],"scalable":[84],"requires":[86],"minimum":[87],"changes":[88],"code.":[92],"overall":[94],"speedup":[95],"realistic":[98],"calculation":[99],"minimizing":[100],"myoglobin":[105],"reaches":[106],"factor":[108],"3":[110],"4":[112],"processors.":[113],"\u00a9":[114],"1994":[115],"by":[116],"John":[117],"Wiley":[118],"&amp;":[119],"Sons,":[120],"Inc.":[121]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
