{"id":"https://openalex.org/W2606142660","doi":"https://doi.org/10.1093/nar/gkx312","title":"LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands","display_name":"LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands","publication_year":2017,"publication_date":"2017-04-20","ids":{"openalex":"https://openalex.org/W2606142660","doi":"https://doi.org/10.1093/nar/gkx312","mag":"2606142660","pmid":"https://pubmed.ncbi.nlm.nih.gov/28444340"},"language":"gl","primary_location":{"id":"doi:10.1093/nar/gkx312","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkx312","pdf_url":"https://academic.oup.com/nar/article-pdf/45/W1/W331/23740908/gkx312.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/45/W1/W331/23740908/gkx312.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062840503","display_name":"Leela S. Dodda","orcid":"https://orcid.org/0000-0002-3584-1729"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leela S. Dodda","raw_affiliation_strings":["Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA","Department of Chemistry, Yale University, New Haven, CT 06520\u20138107, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Chemistry, Yale University, New Haven, CT 06520\u20138107, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029965580","display_name":"Israel Cabeza de Vaca","orcid":"https://orcid.org/0000-0002-6208-1091"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Israel Cabeza\u00a0de\u00a0Vaca","raw_affiliation_strings":["Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA","Department of Chemistry, Yale University, New Haven, CT 06520\u20138107, USA"],"raw_orcid":"https://orcid.org/0000-0002-6208-1091","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Chemistry, Yale University, New Haven, CT 06520\u20138107, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080825811","display_name":"Julian Tirado\u2010Rives","orcid":"https://orcid.org/0000-0001-7330-189X"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julian Tirado-Rives","raw_affiliation_strings":["Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA","Department of Chemistry, Yale University, New Haven, CT 06520\u20138107, USA"],"raw_orcid":"https://orcid.org/0000-0001-7330-189X","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Chemistry, Yale University, New Haven, CT 06520\u20138107, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053850265","display_name":"William L. Jorgensen","orcid":"https://orcid.org/0000-0002-3993-9520"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"William L. Jorgensen","raw_affiliation_strings":["Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA","Department of Chemistry, Yale University, New Haven, CT 06520\u20138107, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Chemistry, Yale University, New Haven, CT 06520\u20138107, USA","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053850265"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":20.3019,"has_fulltext":true,"cited_by_count":1689,"citation_normalized_percentile":{"value":0.99652085,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"45","issue":"W1","first_page":"W331","last_page":"W336"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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/T11162","display_name":"Enzyme Structure and Function","score":0.9984999895095825,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9973000288009644,"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/opls","display_name":"OPLS","score":0.7209774255752563},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.7116722464561462},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.6299964785575867},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5823787450790405},{"id":"https://openalex.org/keywords/intermolecular-force","display_name":"Intermolecular force","score":0.5652225613594055},{"id":"https://openalex.org/keywords/molecular-mechanics","display_name":"Molecular mechanics","score":0.5456255078315735},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.47292807698249817},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4701535701751709},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.46533316373825073},{"id":"https://openalex.org/keywords/nucleic-acid","display_name":"Nucleic acid","score":0.463239848613739},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.4355934262275696},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4068601429462433},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3765857517719269},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.36200064420700073},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.3561273217201233},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.30082520842552185},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.29467740654945374},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.23961997032165527},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14713522791862488},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.13393881916999817},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.12178871035575867},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11584028601646423},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09385302662849426},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.09219697117805481}],"concepts":[{"id":"https://openalex.org/C38660458","wikidata":"https://www.wikidata.org/wiki/Q7072834","display_name":"OPLS","level":4,"score":0.7209774255752563},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.7116722464561462},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.6299964785575867},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5823787450790405},{"id":"https://openalex.org/C166950319","wikidata":"https://www.wikidata.org/wiki/Q245031","display_name":"Intermolecular force","level":3,"score":0.5652225613594055},{"id":"https://openalex.org/C25057246","wikidata":"https://www.wikidata.org/wiki/Q1344441","display_name":"Molecular mechanics","level":3,"score":0.5456255078315735},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.47292807698249817},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4701535701751709},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.46533316373825073},{"id":"https://openalex.org/C24107716","wikidata":"https://www.wikidata.org/wiki/Q123619","display_name":"Nucleic acid","level":2,"score":0.463239848613739},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.4355934262275696},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4068601429462433},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3765857517719269},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.36200064420700073},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3561273217201233},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.30082520842552185},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.29467740654945374},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23961997032165527},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14713522791862488},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.13393881916999817},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.12178871035575867},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11584028601646423},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09385302662849426},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.09219697117805481},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C119049451","wikidata":"https://www.wikidata.org/wiki/Q3318070","display_name":"Water model","level":3,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000880","descriptor_name":"Anthraquinones","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000880","descriptor_name":"Anthraquinones","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000880","descriptor_name":"Anthraquinones","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001547","descriptor_name":"Benzaldehydes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001547","descriptor_name":"Benzaldehydes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001547","descriptor_name":"Benzaldehydes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001559","descriptor_name":"Benzhydryl Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001559","descriptor_name":"Benzhydryl Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001559","descriptor_name":"Benzhydryl Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002733","descriptor_name":"Chlorophenols","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002733","descriptor_name":"Chlorophenols","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002733","descriptor_name":"Chlorophenols","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkx312","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkx312","pdf_url":"https://academic.oup.com/nar/article-pdf/45/W1/W331/23740908/gkx312.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:28444340","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28444340","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,"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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5793816","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5793816","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkx312","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkx312","pdf_url":"https://academic.oup.com/nar/article-pdf/45/W1/W331/23740908/gkx312.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2623812907","display_name":null,"funder_award_id":"R01 GM032136","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6550506410","display_name":null,"funder_award_id":"GM32136","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7816401740","display_name":null,"funder_award_id":"UL1 TR001863","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"}],"funders":[{"id":"https://openalex.org/F4320308380","display_name":"Yale University","ror":"https://ror.org/03v76x132"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332618","display_name":"Faculty of Arts and Sciences","ror":"https://ror.org/03vek6s52"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2606142660.pdf","grobid_xml":"https://content.openalex.org/works/W2606142660.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W77846334","https://openalex.org/W185137928","https://openalex.org/W1031578623","https://openalex.org/W1976203248","https://openalex.org/W1990161102","https://openalex.org/W1997772366","https://openalex.org/W1998931691","https://openalex.org/W2005136695","https://openalex.org/W2008792691","https://openalex.org/W2011703027","https://openalex.org/W2019701333","https://openalex.org/W2021520922","https://openalex.org/W2023735050","https://openalex.org/W2038210983","https://openalex.org/W2041189078","https://openalex.org/W2041791898","https://openalex.org/W2048740371","https://openalex.org/W2050470003","https://openalex.org/W2051381895","https://openalex.org/W2060433756","https://openalex.org/W2060872117","https://openalex.org/W2078409719","https://openalex.org/W2081396007","https://openalex.org/W2103111465","https://openalex.org/W2111131931","https://openalex.org/W2114367386","https://openalex.org/W2118233996","https://openalex.org/W2120869341","https://openalex.org/W2125653280","https://openalex.org/W2132262459","https://openalex.org/W2135974653","https://openalex.org/W2144288821","https://openalex.org/W2149779504","https://openalex.org/W2150981663","https://openalex.org/W2167029191","https://openalex.org/W2168240189","https://openalex.org/W2179425537","https://openalex.org/W2321640944","https://openalex.org/W2323403662","https://openalex.org/W2341723739","https://openalex.org/W2408399550","https://openalex.org/W2420659973","https://openalex.org/W2589236205","https://openalex.org/W7073782271"],"related_works":["https://openalex.org/W1996733108","https://openalex.org/W2007369531","https://openalex.org/W2917147478","https://openalex.org/W1988279278","https://openalex.org/W3213031005","https://openalex.org/W2087197958","https://openalex.org/W2182607276","https://openalex.org/W3087365829","https://openalex.org/W2332365892","https://openalex.org/W2071281986"],"abstract_inverted_index":{"The":[0,68],"accurate":[1],"calculation":[2],"of":[3,19,22,43,54,58,88],"protein/nucleic":[4],"acid-ligand":[5],"interactions":[6,113],"or":[7],"condensed":[8],"phase":[9],"properties":[10],"by":[11],"force":[12,30,79],"field-based":[13],"methods":[14],"require":[15],"a":[16,55],"precise":[17],"description":[18],"the":[20,26,41,44,47,52,62,86],"energetics":[21],"intermolecular":[23,112],"interactions.":[24],"Despite":[25],"progress":[27],"made":[28],"in":[29,85,106],"fields,":[31],"small":[32],"molecule":[33],"parameterization":[34],"remains":[35],"an":[36,73],"open":[37,124],"problem":[38],"due":[39],"to":[40,64,125],"magnitude":[42],"chemical":[45],"space;":[46],"most":[48],"critical":[49],"issue":[50],"is":[51,121],"estimation":[53],"balanced":[56],"set":[57],"atomic":[59],"charges":[60],"with":[61,114],"ability":[63],"reproduce":[65],"experimental":[66],"properties.":[67],"LigParGen":[69],"web":[70],"server":[71,99],"provides":[72],"intuitive":[74],"interface":[75],"for":[76,82,103],"generating":[77],"OPLS-AA/1.14*CM1A(-LBCC)":[78],"field":[80],"parameters":[81],"organic":[83],"ligands,":[84],"formats":[87],"commonly":[89],"used":[90],"molecular":[91,117],"dynamics":[92],"and":[93,123,129],"Monte":[94],"Carlo":[95],"simulation":[96],"packages.":[97],"This":[98],"has":[100,130],"high":[101],"value":[102],"researchers":[104],"interested":[105],"studying":[107],"any":[108],"phenomena":[109],"based":[110],"on":[111],"ligands":[115],"via":[116],"mechanics":[118],"simulations.":[119],"It":[120],"free":[122],"all":[126],"at":[127],"jorgensenresearch.com/ligpargen,":[128],"no":[131],"login":[132],"requirements.":[133]},"counts_by_year":[{"year":2026,"cited_by_count":162},{"year":2025,"cited_by_count":339},{"year":2024,"cited_by_count":351},{"year":2023,"cited_by_count":276},{"year":2022,"cited_by_count":216},{"year":2021,"cited_by_count":164},{"year":2020,"cited_by_count":113},{"year":2019,"cited_by_count":45},{"year":2018,"cited_by_count":20},{"year":2017,"cited_by_count":3}],"updated_date":"2026-06-28T08:01:55.173337","created_date":"2025-10-10T00:00:00"}