{"id":"https://openalex.org/W2964841466","doi":"https://doi.org/10.1186/s13321-019-0371-6","title":"Accuracy evaluation and addition of improved dihedral parameters for the MMFF94s","display_name":"Accuracy evaluation and addition of improved dihedral parameters for the MMFF94s","publication_year":2019,"publication_date":"2019-08-07","ids":{"openalex":"https://openalex.org/W2964841466","doi":"https://doi.org/10.1186/s13321-019-0371-6","mag":"2964841466","pmid":"https://pubmed.ncbi.nlm.nih.gov/31392432"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-019-0371-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0371-6","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0371-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0371-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102723237","display_name":"Jo\u00ebl Wahl","orcid":"https://orcid.org/0000-0002-7904-9637"},"institutions":[{"id":"https://openalex.org/I4210136915","display_name":"Idorsia (Switzerland)","ror":"https://ror.org/03va9ng43","country_code":"CH","type":"company","lineage":["https://openalex.org/I4210136915"]},{"id":"https://openalex.org/I7495430","display_name":"Idiap Research Institute","ror":"https://ror.org/05932h694","country_code":"CH","type":"facility","lineage":["https://openalex.org/I7495430"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Joel Wahl","raw_affiliation_strings":["Scientific Computing Drug Discovery, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 89, 4123, Allschwil, Switzerland. joel.wahl@idorsia.com","Scientific Computing Drug Discovery, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 89, 4123, Allschwil, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-7904-9637","affiliations":[{"raw_affiliation_string":"Scientific Computing Drug Discovery, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 89, 4123, Allschwil, Switzerland. joel.wahl@idorsia.com","institution_ids":["https://openalex.org/I4210136915"]},{"raw_affiliation_string":"Scientific Computing Drug Discovery, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 89, 4123, Allschwil, Switzerland","institution_ids":["https://openalex.org/I7495430","https://openalex.org/I4210136915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081069323","display_name":"Jo\u00ebl Freyss","orcid":"https://orcid.org/0000-0001-8349-1762"},"institutions":[{"id":"https://openalex.org/I4210136915","display_name":"Idorsia (Switzerland)","ror":"https://ror.org/03va9ng43","country_code":"CH","type":"company","lineage":["https://openalex.org/I4210136915"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Joel Freyss","raw_affiliation_strings":["Global Information Systems, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 91, 4123, Allschwil, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-8349-1762","affiliations":[{"raw_affiliation_string":"Global Information Systems, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 91, 4123, Allschwil, Switzerland","institution_ids":["https://openalex.org/I4210136915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062040191","display_name":"Modest von Korff","orcid":"https://orcid.org/0000-0002-2549-8672"},"institutions":[{"id":"https://openalex.org/I4210136915","display_name":"Idorsia (Switzerland)","ror":"https://ror.org/03va9ng43","country_code":"CH","type":"company","lineage":["https://openalex.org/I4210136915"]},{"id":"https://openalex.org/I7495430","display_name":"Idiap Research Institute","ror":"https://ror.org/05932h694","country_code":"CH","type":"facility","lineage":["https://openalex.org/I7495430"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Modest von Korff","raw_affiliation_strings":["Scientific Computing Drug Discovery, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 89, 4123, Allschwil, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-2549-8672","affiliations":[{"raw_affiliation_string":"Scientific Computing Drug Discovery, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 89, 4123, Allschwil, Switzerland","institution_ids":["https://openalex.org/I7495430","https://openalex.org/I4210136915"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102021785","display_name":"Thomas Sander","orcid":"https://orcid.org/0000-0003-4019-1959"},"institutions":[{"id":"https://openalex.org/I4210136915","display_name":"Idorsia (Switzerland)","ror":"https://ror.org/03va9ng43","country_code":"CH","type":"company","lineage":["https://openalex.org/I4210136915"]},{"id":"https://openalex.org/I7495430","display_name":"Idiap Research Institute","ror":"https://ror.org/05932h694","country_code":"CH","type":"facility","lineage":["https://openalex.org/I7495430"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Thomas Sander","raw_affiliation_strings":["Scientific Computing Drug Discovery, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 89, 4123, Allschwil, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-4019-1959","affiliations":[{"raw_affiliation_string":"Scientific Computing Drug Discovery, Idorsia Pharmaceuticals Ltd, Hegenheimermattweg 89, 4123, Allschwil, Switzerland","institution_ids":["https://openalex.org/I7495430","https://openalex.org/I4210136915"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5102723237"],"corresponding_institution_ids":["https://openalex.org/I4210136915","https://openalex.org/I7495430"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":4.8507,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.95502038,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"11","issue":"1","first_page":"53","last_page":"53"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994000196456909,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9973999857902527,"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/dihedral-angle","display_name":"Dihedral angle","score":0.9762549996376038},{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.7610867023468018},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7084076404571533},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.6388733386993408},{"id":"https://openalex.org/keywords/ab-initio","display_name":"Ab initio","score":0.5705874562263489},{"id":"https://openalex.org/keywords/torsion","display_name":"Torsion (gastropod)","score":0.5352815985679626},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5317579507827759},{"id":"https://openalex.org/keywords/minification","display_name":"Minification","score":0.49081143736839294},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.35850638151168823},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3322640657424927},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3074045181274414},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17963212728500366},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.10870528221130371},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.10308980941772461},{"id":"https://openalex.org/keywords/geology","display_name":"Geology","score":0.06837594509124756}],"concepts":[{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.9762549996376038},{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.7610867023468018},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7084076404571533},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.6388733386993408},{"id":"https://openalex.org/C2781442258","wikidata":"https://www.wikidata.org/wiki/Q46310","display_name":"Ab initio","level":2,"score":0.5705874562263489},{"id":"https://openalex.org/C77461463","wikidata":"https://www.wikidata.org/wiki/Q7827201","display_name":"Torsion (gastropod)","level":2,"score":0.5352815985679626},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5317579507827759},{"id":"https://openalex.org/C147764199","wikidata":"https://www.wikidata.org/wiki/Q6865248","display_name":"Minification","level":2,"score":0.49081143736839294},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.35850638151168823},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3322640657424927},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3074045181274414},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17963212728500366},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.10870528221130371},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.10308980941772461},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.06837594509124756},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0},{"id":"https://openalex.org/C141071460","wikidata":"https://www.wikidata.org/wiki/Q40821","display_name":"Surgery","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-019-0371-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0371-6","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0371-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:31392432","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31392432","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:db5d4ce67ab8496cb3ba9c0832a3a257","is_oa":true,"landing_page_url":"https://doaj.org/article/db5d4ce67ab8496cb3ba9c0832a3a257","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 11, Iss 1, Pp 1-10 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5640276","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6686419","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-019-0371-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0371-6","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0371-6","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2964841466.pdf","grobid_xml":"https://content.openalex.org/works/W2964841466.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1971572370","https://openalex.org/W1971849220","https://openalex.org/W1985588649","https://openalex.org/W1995850373","https://openalex.org/W2000815209","https://openalex.org/W2001428495","https://openalex.org/W2004145462","https://openalex.org/W2037993052","https://openalex.org/W2042572511","https://openalex.org/W2052818547","https://openalex.org/W2057491831","https://openalex.org/W2058653824","https://openalex.org/W2063779505","https://openalex.org/W2067687494","https://openalex.org/W2070753604","https://openalex.org/W2071579644","https://openalex.org/W2077467665","https://openalex.org/W2087925988","https://openalex.org/W2089974748","https://openalex.org/W2098959735","https://openalex.org/W2100125011","https://openalex.org/W2102887337","https://openalex.org/W2109225217","https://openalex.org/W2111158634","https://openalex.org/W2121853844","https://openalex.org/W2127463492","https://openalex.org/W2132262459","https://openalex.org/W2135873580","https://openalex.org/W2144571979","https://openalex.org/W2147421370","https://openalex.org/W2147993766","https://openalex.org/W2155430111","https://openalex.org/W2158219301","https://openalex.org/W2159010139","https://openalex.org/W2166114438","https://openalex.org/W2170869859","https://openalex.org/W2171047927","https://openalex.org/W2222589778","https://openalex.org/W2244785476","https://openalex.org/W2261529249","https://openalex.org/W2587816047","https://openalex.org/W2589236205","https://openalex.org/W2596982648","https://openalex.org/W2613133334","https://openalex.org/W2613477619","https://openalex.org/W2630248196"],"related_works":["https://openalex.org/W2023036309","https://openalex.org/W2128884622","https://openalex.org/W2112380088","https://openalex.org/W1715467939","https://openalex.org/W3012606738","https://openalex.org/W1972863456","https://openalex.org/W2089371831","https://openalex.org/W4318816969","https://openalex.org/W2148970764","https://openalex.org/W2011402683"],"abstract_inverted_index":{"The":[0],"Platinum":[1],"dataset":[2],"of":[3,13,24,57],"protein-bound":[4],"ligand":[5],"conformations":[6,21],"was":[7],"used":[8],"to":[9,18],"benchmark":[10],"the":[11,14,47],"ability":[12],"MMFF94s":[15],"force":[16],"field":[17],"generate":[19],"bioactive":[20],"by":[22,38],"minimization":[23],"randomly":[25],"generated":[26,58],"conformers.":[27],"Torsion":[28],"angle":[29],"parameters":[30],"that":[31],"generally":[32],"caused":[33],"wrong":[34],"geometries":[35],"were":[36],"reparameterized":[37],"conducting":[39],"dihedral":[40],"scans":[41],"using":[42],"ab":[43],"initio":[44],"calculations":[45],"at":[46],"MP2":[48],"level.":[49],"This":[50],"reparameterization":[51],"resulted":[52],"in":[53],"a":[54],"systematic":[55],"improvement":[56],"conformations.":[59]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":9}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
