{"id":"https://openalex.org/W2158219301","doi":"https://doi.org/10.1186/s13321-014-0037-3","title":"Bringing the MMFF force field to the RDKit: implementation and validation","display_name":"Bringing the MMFF force field to the RDKit: implementation and validation","publication_year":2014,"publication_date":"2014-07-10","ids":{"openalex":"https://openalex.org/W2158219301","doi":"https://doi.org/10.1186/s13321-014-0037-3","mag":"2158219301"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-014-0037-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-014-0037-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-014-0037-3","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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-014-0037-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038418094","display_name":"Paolo Tosco","orcid":"https://orcid.org/0000-0002-0034-9494"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Paolo Tosco","raw_affiliation_strings":["Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, Torino, 10125, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, Torino, 10125, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057292715","display_name":"Nikolaus Stiefl","orcid":"https://orcid.org/0000-0003-2562-7080"},"institutions":[{"id":"https://openalex.org/I1283582996","display_name":"Novartis (Switzerland)","ror":"https://ror.org/02f9zrr09","country_code":"CH","type":"company","lineage":["https://openalex.org/I1283582996"]},{"id":"https://openalex.org/I4400600974","display_name":"Novartis Institutes for BioMedical Research","ror":"https://ror.org/053gv2m95","country_code":null,"type":"funder","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4400600974"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Nikolaus Stiefl","raw_affiliation_strings":["Novartis Institutes for Biomedical Research, Basel, CH-4002, Switzerland"],"affiliations":[{"raw_affiliation_string":"Novartis Institutes for Biomedical Research, Basel, CH-4002, Switzerland","institution_ids":["https://openalex.org/I1283582996","https://openalex.org/I4400600974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056808182","display_name":"Gregory A. Landrum","orcid":"https://orcid.org/0000-0001-6279-4481"},"institutions":[{"id":"https://openalex.org/I4400600974","display_name":"Novartis Institutes for BioMedical Research","ror":"https://ror.org/053gv2m95","country_code":null,"type":"funder","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4400600974"]},{"id":"https://openalex.org/I1283582996","display_name":"Novartis (Switzerland)","ror":"https://ror.org/02f9zrr09","country_code":"CH","type":"company","lineage":["https://openalex.org/I1283582996"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Gregory Landrum","raw_affiliation_strings":["Novartis Institutes for Biomedical Research, Basel, CH-4002, Switzerland"],"affiliations":[{"raw_affiliation_string":"Novartis Institutes for Biomedical Research, Basel, CH-4002, Switzerland","institution_ids":["https://openalex.org/I1283582996","https://openalex.org/I4400600974"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5038418094"],"corresponding_institution_ids":["https://openalex.org/I55143463"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":2.2816,"has_fulltext":true,"cited_by_count":262,"citation_normalized_percentile":{"value":0.88675876,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"6","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9983999729156494,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7736817598342896},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7724024057388306},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.6984493732452393},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.6511902213096619},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.5788013935089111},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.552290678024292},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.49592098593711853},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4702438414096832},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4673096835613251},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4418228268623352},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.4317472577095032},{"id":"https://openalex.org/keywords/workbench","display_name":"Workbench","score":0.4229370355606079},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.34696751832962036},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3151143193244934},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2236175537109375},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21110743284225464},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.19696465134620667},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.19536656141281128},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12963473796844482}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7736817598342896},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7724024057388306},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.6984493732452393},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.6511902213096619},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.5788013935089111},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.552290678024292},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.49592098593711853},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4702438414096832},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4673096835613251},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4418228268623352},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.4317472577095032},{"id":"https://openalex.org/C2779145975","wikidata":"https://www.wikidata.org/wiki/Q347690","display_name":"Workbench","level":3,"score":0.4229370355606079},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.34696751832962036},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3151143193244934},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2236175537109375},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21110743284225464},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.19696465134620667},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.19536656141281128},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12963473796844482},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1186/s13321-014-0037-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-014-0037-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-014-0037-3","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":"pmh:oai:europepmc.org:3094635","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4116604","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/s13321-014-0037-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-014-0037-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-014-0037-3","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":[{"id":"https://metadata.un.org/sdg/7","score":0.6399999856948853,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320333796","display_name":"Novartis Institutes for BioMedical Research","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2158219301.pdf","grobid_xml":"https://content.openalex.org/works/W2158219301.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W153460014","https://openalex.org/W1971572370","https://openalex.org/W2030971064","https://openalex.org/W2051381895","https://openalex.org/W2054881399","https://openalex.org/W2057491831","https://openalex.org/W2070753604","https://openalex.org/W2071579644","https://openalex.org/W2102887337","https://openalex.org/W2121853844","https://openalex.org/W2144571979","https://openalex.org/W2147421370","https://openalex.org/W2147993766","https://openalex.org/W2166114438","https://openalex.org/W2169678694"],"related_works":["https://openalex.org/W2388509490","https://openalex.org/W2109648960","https://openalex.org/W1573015311","https://openalex.org/W2166015079","https://openalex.org/W2050384624","https://openalex.org/W2776888796","https://openalex.org/W2388480422","https://openalex.org/W2013194361","https://openalex.org/W2562353568","https://openalex.org/W189850294"],"abstract_inverted_index":{"Abstract":[0],"A":[1],"general":[2],"purpose":[3],"force":[4,38,97],"field":[5,39],"such":[6],"as":[7],"MMFF94/MMFF94s,":[8],"which":[9],"can":[10,47],"properly":[11],"deal":[12],"with":[13,144],"a":[14,27,51,138],"wide":[15],"range":[16],"of":[17,26,36,61,137,147],"diverse":[18],"structures,":[19],"is":[20,157],"very":[21],"valuable":[22],"in":[23,68,162],"the":[24,41,59,62,69,77,83,113,124,145,148,154],"context":[25],"cheminformatics":[28],"toolkit.":[29],"Herein":[30],"we":[31],"present":[32],"an":[33],"open-source":[34],"implementation":[35,72],"this":[37],"within":[40],"RDKit.":[42,70],"The":[43,135],"new":[44],"MMFF":[45,84,125],"functionality":[46,150],"be":[48],"accessed":[49],"through":[50],"C++/C#/Python/Java":[52],"application":[53],"programming":[54],"interface":[55],"(API)":[56],"developed":[57],"along":[58],"lines":[60],"one":[63],"already":[64],"available":[65,114],"for":[66,102],"UFF":[67],"Our":[71],"was":[73],"fully":[74],"validated":[75],"against":[76],"official":[78],"validation":[79],"suite":[80],"provided":[81],"by":[82,153],"authors.":[85],"All":[86],"energies":[87],"and":[88,96,128,151,165],"gradients":[89],"were":[90,99],"correctly":[91,100],"computed;":[92],"moreover,":[93],"atom":[94],"type":[95],"constants":[98],"assigned":[101],"3D":[103],"molecules":[104],"built":[105],"from":[106,123],"SMILES":[107],"strings.":[108],"To":[109],"provide":[110],"full":[111],"flexibility,":[112],"API":[115],"provides":[116],"direct":[117],"access":[118],"to":[119,129,159],"include/exclude":[120],"individual":[121],"terms":[122],"energy":[126],"expression":[127],"carry":[130],"out":[131],"constrained":[132],"geometry":[133],"optimizations.":[134],"availability":[136],"MMFF-capable":[139],"molecular":[140],"mechanics":[141],"engine":[142],"coupled":[143],"rest":[146],"RDKit":[149],"covered":[152],"BSD":[155],"license":[156],"appealing":[158],"researchers":[160],"operating":[161],"both":[163],"academia":[164],"industry.":[166]},"counts_by_year":[{"year":2026,"cited_by_count":20},{"year":2025,"cited_by_count":53},{"year":2024,"cited_by_count":40},{"year":2023,"cited_by_count":46},{"year":2022,"cited_by_count":23},{"year":2021,"cited_by_count":26},{"year":2020,"cited_by_count":18},{"year":2019,"cited_by_count":17},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":5}],"updated_date":"2026-04-07T14:57:38.498316","created_date":"2025-10-10T00:00:00"}