{"id":"https://openalex.org/W2069123478","doi":"https://doi.org/10.1002/jcc.10349","title":"A point\u2010charge force field for molecular mechanics simulations of proteins based on condensed\u2010phase quantum mechanical calculations","display_name":"A point\u2010charge force field for molecular mechanics simulations of proteins based on condensed\u2010phase quantum mechanical calculations","publication_year":2003,"publication_date":"2003-09-25","ids":{"openalex":"https://openalex.org/W2069123478","doi":"https://doi.org/10.1002/jcc.10349","mag":"2069123478","pmid":"https://pubmed.ncbi.nlm.nih.gov/14531054"},"language":"en","primary_location":{"id":"doi:10.1002/jcc.10349","doi":"https://doi.org/10.1002/jcc.10349","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.10349","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,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"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"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"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/A5016265600","display_name":"Yong Duan","orcid":"https://orcid.org/0000-0003-3793-5099","observed_orcids":["https://orcid.org/0000-0003-3793-5099","https://orcid.org/0009-0008-4393-2090"]},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yong Duan","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA. yduan@udel.edu","Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, 19716, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA. yduan@udel.edu","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, 19716, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031292318","display_name":"Chun Fu Wu","orcid":"https://orcid.org/0000-0002-0176-3873","observed_orcids":["https://orcid.org/0000-0002-0176-3873"]},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chun Wu","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","University of Delaware"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042267427","display_name":"Shibasish Chowdhury","orcid":"https://orcid.org/0000-0001-9290-3802","observed_orcids":["https://orcid.org/0000-0001-9290-3802"]},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shibasish Chowdhury","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","University of Delaware"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035535436","display_name":"Mathew C. Lee","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mathew C. Lee","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","University of Delaware"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102196477","display_name":"Guoming Xiong","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guoming Xiong","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","University of Delaware"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065579191","display_name":"Wei Zhang","orcid":"https://orcid.org/0000-0001-7134-5290","observed_orcids":["https://orcid.org/0000-0001-7134-5290"]},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Zhang","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","University of Delaware"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101918321","display_name":"Rong Yang","orcid":"https://orcid.org/0000-0002-6029-1343","observed_orcids":["https://orcid.org/0000-0002-6029-1343"]},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rong Yang","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","University of Delaware"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716","institution_ids":["https://openalex.org/I86501945"]},{"raw_affiliation_string":"University of Delaware","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032185922","display_name":"Piotr Cieplak","orcid":"https://orcid.org/0000-0003-0700-5691","observed_orcids":["https://orcid.org/0000-0003-0700-5691"]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I4387156175","display_name":"BIOVIA","ror":"https://ror.org/035v3d332","country_code":null,"type":"company","lineage":["https://openalex.org/I4387156175","https://openalex.org/I47431100"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Piotr Cieplak","raw_affiliation_strings":["Accelrys Inc., 9685 Scranton Rd, San Diego, California 92121","Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","Accelrys Inc","University of California at San Francisco"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Accelrys Inc., 9685 Scranton Rd, San Diego, California 92121","institution_ids":["https://openalex.org/I4387156175"]},{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Accelrys Inc","institution_ids":["https://openalex.org/I4387156175"]},{"raw_affiliation_string":"University of California at San Francisco","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032088629","display_name":"Ray Luo","orcid":"https://orcid.org/0000-0002-6346-8271","observed_orcids":["https://orcid.org/0000-0002-6346-8271"]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ray Luo","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","University of California at San Francisco,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"University of California at San Francisco,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029666960","display_name":"Tai\u2010Sung Lee","orcid":"https://orcid.org/0000-0003-2110-2279","observed_orcids":["https://orcid.org/0000-0003-2110-2279"]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I4387156175","display_name":"BIOVIA","ror":"https://ror.org/035v3d332","country_code":null,"type":"company","lineage":["https://openalex.org/I4387156175","https://openalex.org/I47431100"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Taisung Lee","raw_affiliation_strings":["Accelrys Inc., 9685 Scranton Rd, San Diego, California 92121","Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","Accelrys Inc","University of California at San Francisco"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Accelrys Inc., 9685 Scranton Rd, San Diego, California 92121","institution_ids":["https://openalex.org/I4387156175"]},{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Accelrys Inc","institution_ids":["https://openalex.org/I4387156175"]},{"raw_affiliation_string":"University of California at San Francisco","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113544693","display_name":"James W. Caldwell","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Caldwell","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","University of California at San Francisco,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"University of California at San Francisco,","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100643054","display_name":"Junmei Wang","orcid":"https://orcid.org/0000-0002-9607-8229","observed_orcids":["https://orcid.org/0000-0002-9607-8229","https://orcid.org/0009-0007-6115-5152","https://orcid.org/0000-0002-8336-9457"]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junmei Wang","raw_affiliation_strings":["Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","The Green Center for Systems Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"The Green Center for Systems Biology","institution_ids":["https://openalex.org/I4210155419"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112793169","display_name":"Peter A. Kollman","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter Kollman","raw_affiliation_strings":["Deceased","Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","University of California at San Francisco,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Deceased","institution_ids":[]},{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94143","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"University of California at San Francisco,","institution_ids":["https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5016265600"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":{"value":4520,"currency":"USD","value_usd":4520},"apc_paid":null,"fwci":9.0074,"has_fulltext":false,"cited_by_count":4442,"citation_normalized_percentile":{"value":0.9886277,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"16","first_page":"1999","last_page":"2012"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9945999979972839,"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":0.9945999979972839,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.0034000000450760126,"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"}},{"id":"https://openalex.org/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-force-fields","display_name":"protein force fields","score":0.7940000295639038},{"id":"https://openalex.org/keywords/all-atom-force-field","display_name":"all-atom force field","score":0.8220000267028809},{"id":"https://openalex.org/keywords/force-field-parameterization","display_name":"force field parameterization","score":0.7170000076293945},{"id":"https://openalex.org/keywords/electrostatic-potential","display_name":"electrostatic potential","score":0.5920000076293945},{"id":"https://openalex.org/keywords/continuum-solvation-models","display_name":"continuum solvent model","score":0.722000002861023},{"id":"https://openalex.org/keywords/effective-permittivity","display_name":"effective permittivity","score":0.8880000114440918},{"id":"https://openalex.org/keywords/ramachandran-map","display_name":"Ramachandran map","score":0.7820000052452087},{"id":"https://openalex.org/keywords/polyproline-helix","display_name":"polyproline helix","score":0.7089999914169312},{"id":"https://openalex.org/keywords/peptide-conformation","display_name":"peptide conformation","score":0.503000020980835},{"id":"https://openalex.org/keywords/ligand-binding","display_name":"ligand binding","score":0.7289999723434448}],"concepts":[{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.7708802223205566},{"id":"https://openalex.org/C173523689","wikidata":"https://www.wikidata.org/wiki/Q215589","display_name":"Dipole","level":2,"score":0.605581521987915},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.6030518412590027},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5951780080795288},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.5272849202156067},{"id":"https://openalex.org/C175749648","wikidata":"https://www.wikidata.org/wiki/Q1068091","display_name":"Point particle","level":2,"score":0.4935265779495239},{"id":"https://openalex.org/C77461463","wikidata":"https://www.wikidata.org/wiki/Q7827201","display_name":"Torsion (gastropod)","level":2,"score":0.45649898052215576},{"id":"https://openalex.org/C25057246","wikidata":"https://www.wikidata.org/wiki/Q1344441","display_name":"Molecular mechanics","level":3,"score":0.4544716775417328},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4283922016620636},{"id":"https://openalex.org/C117626034","wikidata":"https://www.wikidata.org/wiki/Q26336","display_name":"Electrostatics","level":2,"score":0.4114440977573395},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.3975144326686859},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3346762955188751},{"id":"https://openalex.org/C41999313","wikidata":"https://www.wikidata.org/wiki/Q489328","display_name":"Molecular physics","level":1,"score":0.3315013349056244},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.26608753204345703},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.1846071183681488},{"id":"https://openalex.org/C141071460","wikidata":"https://www.wikidata.org/wiki/Q40821","display_name":"Surgery","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}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002627","descriptor_name":"Chemistry, Physical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002627","descriptor_name":"Chemistry, Physical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002627","descriptor_name":"Chemistry, Physical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004151","descriptor_name":"Dipeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004151","descriptor_name":"Dipeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004151","descriptor_name":"Dipeptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008432","descriptor_name":"Mathematical Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008432","descriptor_name":"Mathematical Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008432","descriptor_name":"Mathematical Computing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055598","descriptor_name":"Chemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055598","descriptor_name":"Chemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055598","descriptor_name":"Chemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1002/jcc.10349","doi":"https://doi.org/10.1002/jcc.10349","is_oa":false,"landing_page_url":"https://doi.org/10.1002/jcc.10349","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,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","medline","norway-1","poland-100","russia-white-list-1","vabb-shw"],"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":"pmid:14531054","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/14531054","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"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":[],"sustainable_development_goals_aurora":[{"score":0.8199999928474426,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G2304411360","display_name":null,"funder_award_id":"GM-67168","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3026246550","display_name":null,"funder_award_id":"GM29072","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3278777692","display_name":null,"funder_award_id":"GM-64458","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6485018044","display_name":null,"funder_award_id":"CRR-15588","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1539434723","https://openalex.org/W1966666354","https://openalex.org/W1966743338","https://openalex.org/W1970683586","https://openalex.org/W1976161355","https://openalex.org/W1976499671","https://openalex.org/W1978885914","https://openalex.org/W1979395376","https://openalex.org/W1984614201","https://openalex.org/W1989945804","https://openalex.org/W1992422451","https://openalex.org/W1993077801","https://openalex.org/W1993227183","https://openalex.org/W2012418922","https://openalex.org/W2013507130","https://openalex.org/W2015697285","https://openalex.org/W2018312454","https://openalex.org/W2023271753","https://openalex.org/W2023477917","https://openalex.org/W2025624195","https://openalex.org/W2027095682","https://openalex.org/W2035687084","https://openalex.org/W2038083805","https://openalex.org/W2040186907","https://openalex.org/W2040823078","https://openalex.org/W2041834854","https://openalex.org/W2042490093","https://openalex.org/W2043454078","https://openalex.org/W2044601459","https://openalex.org/W2051381895","https://openalex.org/W2054881399","https://openalex.org/W2055563809","https://openalex.org/W2067687494","https://openalex.org/W2067769676","https://openalex.org/W2069288013","https://openalex.org/W2073328513","https://openalex.org/W2074661415","https://openalex.org/W2074986801","https://openalex.org/W2083232514","https://openalex.org/W2083624153","https://openalex.org/W2088428564","https://openalex.org/W2091425513","https://openalex.org/W2092067563","https://openalex.org/W2093061282","https://openalex.org/W2101348065","https://openalex.org/W2107952203","https://openalex.org/W2113270377","https://openalex.org/W2122199548","https://openalex.org/W2122220546","https://openalex.org/W2124709367","https://openalex.org/W2129071110","https://openalex.org/W2133230269","https://openalex.org/W2134544924","https://openalex.org/W2137322489","https://openalex.org/W2137736208","https://openalex.org/W2143981217","https://openalex.org/W2153153865","https://openalex.org/W2155524113"],"related_works":["https://openalex.org/W1996733108","https://openalex.org/W2007369531","https://openalex.org/W1988279278","https://openalex.org/W2182607276","https://openalex.org/W4294771207","https://openalex.org/W2081461182","https://openalex.org/W2158570022","https://openalex.org/W2036866634","https://openalex.org/W2129071110","https://openalex.org/W2069939770"],"abstract_inverted_index":{"Molecular":[0],"mechanics":[1],"models":[2,113],"have":[3],"been":[4],"applied":[5],"extensively":[6],"to":[7,45,65,221],"study":[8],"the":[9,19,31,38,46,66,86,107,156,159,180,201,222,227],"dynamics":[10],"of":[11,21,34,49,69,119,137,144,153,172,229,238],"proteins":[12,239],"and":[13,71,114,158,167,182,186,203],"nucleic":[14],"acids.":[15],"Here":[16],"we":[17],"report":[18],"development":[20],"a":[22,151,218,235],"third-generation":[23],"point-charge":[24],"all-atom":[25],"force":[26,96,127,139,224],"field":[27,128,225],"for":[28,164],"proteins.":[29,145],"Following":[30],"earlier":[32],"approach":[33],"Cornell":[35,204],"et":[36,205],"al.,":[37],"charge":[39,207],"set":[40,130,237],"was":[41],"obtained":[42,62],"by":[43,63,211],"fitting":[44,64],"electrostatic":[47],"potentials":[48],"dipeptides":[50],"calculated":[51,74,157],"using":[52,75],"B3LYP/cc-pVTZ//HF/6-31G**":[53],"quantum":[54,77,101],"mechanical":[55,78,102],"methods.":[56,79],"The":[57,91],"main-chain":[58],"torsion":[59],"parameters":[60,82],"were":[61,83,104],"energy":[67],"profiles":[68],"Ace-Ala-Nme":[70,168],"Ace-Gly-Nme":[72,166],"di-peptides":[73],"MP2/cc-pVTZ//HF/6-31G**":[76],"All":[80],"other":[81],"taken":[84],"from":[85,94],"existing":[87],"AMBER":[88],"data":[89],"base.":[90],"major":[92],"departure":[93],"previous":[95,138],"fields":[97,140],"is":[98],"that":[99,125],"all":[100],"calculations":[103],"done":[105],"in":[106,141,193,226],"condensed":[108],"phase":[109],"with":[110,195],"continuum":[111],"solvent":[112],"an":[115],"effective":[116],"dielectric":[117],"constant":[118],"epsilon":[120],"=":[121],"4.":[122],"We":[123],"anticipate":[124],"this":[126],"parameter":[129],"will":[131],"address":[132],"certain":[133],"critical":[134],"short":[135],"comings":[136],"condensed-phase":[142],"simulations":[143,233],"Initial":[146],"tests":[147],"on":[148,234],"peptides":[149],"demonstrated":[150],"high-degree":[152],"similarity":[154],"between":[155,179,200,214],"statistically":[160],"measured":[161],"Ramanchandran":[162],"maps":[163],"both":[165],"di-peptides.":[169],"Some":[170],"highlights":[171],"our":[173],"results":[174],"include":[175],"(1)":[176],"well-preserved":[177],"balance":[178],"extended":[181],"helical":[183,191],"region":[184,192],"distributions,":[185],"(2)":[187],"favorable":[188],"type-II":[189],"poly-proline":[190],"agreement":[194,213],"recent":[196],"experiments.":[197],"Backward":[198],"compatibility":[199],"new":[202,223],"al.":[206],"sets,":[208],"as":[209],"judged":[210],"overall":[212],"dipole":[215],"moments,":[216],"allows":[217],"smooth":[219],"transition":[220],"area":[228],"ligand-binding":[230],"calculations.":[231],"Test":[232],"large":[236],"are":[240],"also":[241],"discussed.":[242]},"counts_by_year":[{"year":2026,"cited_by_count":78},{"year":2025,"cited_by_count":140},{"year":2024,"cited_by_count":124},{"year":2023,"cited_by_count":167},{"year":2022,"cited_by_count":208},{"year":2021,"cited_by_count":211},{"year":2020,"cited_by_count":180},{"year":2019,"cited_by_count":265},{"year":2018,"cited_by_count":225},{"year":2017,"cited_by_count":255},{"year":2016,"cited_by_count":289},{"year":2015,"cited_by_count":313},{"year":2014,"cited_by_count":355},{"year":2013,"cited_by_count":334},{"year":2012,"cited_by_count":328}],"updated_date":"2026-10-15T10:00:46.086208","created_date":"2016-06-24T00:00:00"}