{"id":"https://openalex.org/W2104630281","doi":"https://doi.org/10.1021/acs.jcim.5b00368","title":"FESetup: Automating Setup for Alchemical Free Energy Simulations","display_name":"FESetup: Automating Setup for Alchemical Free Energy Simulations","publication_year":2015,"publication_date":"2015-11-06","ids":{"openalex":"https://openalex.org/W2104630281","doi":"https://doi.org/10.1021/acs.jcim.5b00368","mag":"2104630281","pmid":"https://pubmed.ncbi.nlm.nih.gov/26544598"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5b00368","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00368","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.pure.ed.ac.uk/ws/files/23507572/s1_ln1939358_979811707_1939656818Hwf1521014188IdV17396359811939358PDF_HI0001.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024497714","display_name":"Hannes H. Loeffler","orcid":"https://orcid.org/0000-0001-9458-3945"},"institutions":[{"id":"https://openalex.org/I2802015276","display_name":"Daresbury Laboratory","ror":"https://ror.org/0089bg420","country_code":"GB","type":"facility","lineage":["https://openalex.org/I162524378","https://openalex.org/I2802015276","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Hannes H. Loeffler","raw_affiliation_strings":["Scientific\rComputing Department, STFC Daresbury, Keckwick Lane, Warrington WA4 4AD, United Kingdom","Scientific Computing Department, STFC Daresbury , Keckwick Lane, Warrington WA4 4AD, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Scientific\rComputing Department, STFC Daresbury, Keckwick Lane, Warrington WA4 4AD, United Kingdom","institution_ids":["https://openalex.org/I2802015276"]},{"raw_affiliation_string":"Scientific Computing Department, STFC Daresbury , Keckwick Lane, Warrington WA4 4AD, United Kingdom","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041098529","display_name":"Julien Michel","orcid":"https://orcid.org/0000-0003-0360-1760"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Julien Michel","raw_affiliation_strings":["EaStCHEM\rSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom","EaStCHEM, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom"],"affiliations":[{"raw_affiliation_string":"EaStCHEM\rSchool of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"EaStCHEM, School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, United Kingdom","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034343670","display_name":"Christopher Woods","orcid":"https://orcid.org/0000-0001-6563-9903"},"institutions":[{"id":"https://openalex.org/I36234482","display_name":"University of Bristol","ror":"https://ror.org/0524sp257","country_code":"GB","type":"education","lineage":["https://openalex.org/I36234482"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christopher Woods","raw_affiliation_strings":["BrisSynBio, University of Bristol, 8\u221210\rBerkeley Square, Bristol BS8 1HH, United Kingdom","BrisSynBio, University of Bristol , 8-10 Berkeley Square, Bristol BS8 1HH, United Kingdom"],"affiliations":[{"raw_affiliation_string":"BrisSynBio, University of Bristol, 8\u221210\rBerkeley Square, Bristol BS8 1HH, United Kingdom","institution_ids":["https://openalex.org/I36234482"]},{"raw_affiliation_string":"BrisSynBio, University of Bristol , 8-10 Berkeley Square, Bristol BS8 1HH, United Kingdom","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5024497714"],"corresponding_institution_ids":["https://openalex.org/I2802015276"],"apc_list":null,"apc_paid":null,"fwci":4.3763,"has_fulltext":true,"cited_by_count":122,"citation_normalized_percentile":{"value":0.95073724,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"55","issue":"12","first_page":"2485","last_page":"2490"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9962999820709229,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9955000281333923,"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/alchemy","display_name":"Alchemy","score":0.6198174357414246},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.560257077217102},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5425345301628113},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.0952908992767334},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.07594236731529236},{"id":"https://openalex.org/keywords/art","display_name":"Art","score":0.06652066111564636},{"id":"https://openalex.org/keywords/art-history","display_name":"Art history","score":0.05894455313682556}],"concepts":[{"id":"https://openalex.org/C174468945","wikidata":"https://www.wikidata.org/wiki/Q39689","display_name":"Alchemy","level":2,"score":0.6198174357414246},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.560257077217102},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5425345301628113},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0952908992767334},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.07594236731529236},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.06652066111564636},{"id":"https://openalex.org/C52119013","wikidata":"https://www.wikidata.org/wiki/Q50637","display_name":"Art history","level":1,"score":0.05894455313682556}],"mesh":[{"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":"D013816","descriptor_name":"Thermodynamics","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":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.5b00368","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00368","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:26544598","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26544598","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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:pure.ed.ac.uk:publications/7bcda8a4-dff9-446b-9d43-3f9ea02a9326","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/7bcda8a4-dff9-446b-9d43-3f9ea02a9326","pdf_url":"https://www.pure.ed.ac.uk/ws/files/23507572/s1_ln1939358_979811707_1939656818Hwf1521014188IdV17396359811939358PDF_HI0001.pdf","source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:purl.org/net/epubs:work/24092508","is_oa":false,"landing_page_url":"http://purl.org/net/epubs/work/24092508","pdf_url":null,"source":{"id":"https://openalex.org/S4306400600","display_name":"ePubs (Science and Technology Facilities Council, Research Councils UK)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I162524378","host_organization_name":"Science and Technology Facilities Council","host_organization_lineage":["https://openalex.org/I162524378"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pure.ed.ac.uk:publications/7bcda8a4-dff9-446b-9d43-3f9ea02a9326","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/7bcda8a4-dff9-446b-9d43-3f9ea02a9326","pdf_url":"https://www.pure.ed.ac.uk/ws/files/23507572/s1_ln1939358_979811707_1939656818Hwf1521014188IdV17396359811939358PDF_HI0001.pdf","source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.8500000238418579,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G1015763213","display_name":null,"funder_award_id":"BB/L01386X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G1361938442","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G1592560434","display_name":null,"funder_award_id":"EP/G042853/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G1717999737","display_name":null,"funder_award_id":"BB/L018756/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G1954672288","display_name":"BrisSynBio: Bristol Centre for Synthetic Biology","funder_award_id":"BB/L01386X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2467146873","display_name":"Inquire: Software for real-time analysis of binding","funder_award_id":"BB/K016601/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G271256356","display_name":null,"funder_award_id":"EP/E022197/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G3583580618","display_name":null,"funder_award_id":"BB/K016601/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G3889144934","display_name":null,"funder_award_id":"EP/G002843/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4706702539","display_name":"CCP-BioSim: Biomolecular Simulation at the Life Sciences Interface","funder_award_id":"EP/M022609/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4727989359","display_name":"CCP-BioSim: Biomolecular simulation at the life sciences interface","funder_award_id":"EP/J010588/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5192625861","display_name":null,"funder_award_id":"EP/M015378/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5758995618","display_name":null,"funder_award_id":"EP/M022609/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6148688325","display_name":null,"funder_award_id":"EP/M027546/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7814653466","display_name":null,"funder_award_id":"EP/I030395/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G783393384","display_name":null,"funder_award_id":"EP/J010588/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8294306494","display_name":null,"funder_award_id":"EP/G007705/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8452545418","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8947107902","display_name":null,"funder_award_id":"EP/L000253/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320334632","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61"},{"id":"https://openalex.org/F4320336706","display_name":"BrisSynBio","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2104630281.pdf","grobid_xml":"https://content.openalex.org/works/W2104630281.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1901242010","https://openalex.org/W1964245683","https://openalex.org/W1966509953","https://openalex.org/W1976161355","https://openalex.org/W1978330227","https://openalex.org/W2004124673","https://openalex.org/W2008505552","https://openalex.org/W2014060139","https://openalex.org/W2023182702","https://openalex.org/W2025006523","https://openalex.org/W2041293484","https://openalex.org/W2050122005","https://openalex.org/W2053379287","https://openalex.org/W2072256473","https://openalex.org/W2072683434","https://openalex.org/W2081775931","https://openalex.org/W2093755925","https://openalex.org/W2098943363","https://openalex.org/W2099282863","https://openalex.org/W2103626206","https://openalex.org/W2118233996","https://openalex.org/W2131643298","https://openalex.org/W2132262459","https://openalex.org/W2139447954","https://openalex.org/W2139531945","https://openalex.org/W2140841928","https://openalex.org/W2141155664","https://openalex.org/W2147993766","https://openalex.org/W2150981663","https://openalex.org/W2153747625","https://openalex.org/W2163145888","https://openalex.org/W2169678694","https://openalex.org/W2171268876","https://openalex.org/W2321484219","https://openalex.org/W2327581403","https://openalex.org/W2330799739","https://openalex.org/W2402625670","https://openalex.org/W2419272886"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2327690717","https://openalex.org/W1570968926","https://openalex.org/W2033179625","https://openalex.org/W2047294527","https://openalex.org/W4253737202","https://openalex.org/W2367275899","https://openalex.org/W599555033"],"abstract_inverted_index":{"FESetup":[0],"is":[1,112],"a":[2,61,68],"new":[3],"pipeline":[4],"tool":[5,15],"which":[6],"can":[7,45,81],"be":[8,46,82],"used":[9,83],"flexibly":[10],"within":[11],"larger":[12],"workflows.":[13],"The":[14,119],"aims":[16],"to":[17,87],"support":[18],"fast":[19],"and":[20,43,57,108,126],"easy":[21],"setup":[22,90],"of":[23,102,105],"alchemical":[24],"free":[25,88],"energy":[26,89],"simulations":[27],"for":[28,60,84],"molecular":[29,77],"simulation":[30],"packages":[31],"such":[32],"as":[33,49],"AMBER,":[34],"GROMACS,":[35],"Sire,":[36],"or":[37,91],"NAMD.":[38],"Post-processing":[39],"methods":[40],"like":[41],"MM-PBSA":[42],"LIE":[44],"set":[47],"up":[48],"well.":[50],"Ligands":[51],"are":[52,65,99,114],"automatically":[53],"parametrized":[54],"with":[55,67],"AM1-BCC,":[56],"atom":[58],"mappings":[59],"single":[62],"topology":[63],"description":[64],"computed":[66],"maximum":[69],"common":[70],"substructure":[71],"search":[72],"(MCSS)":[73],"algorithm.":[74],"An":[75],"abstract":[76],"dynamics":[78],"(MD)":[79],"engine":[80],"equilibration":[85],"prior":[86],"standalone.":[92],"Currently,":[93],"all":[94],"modern":[95],"AMBER":[96],"force":[97],"fields":[98],"supported.":[100],"Ease":[101],"use,":[103],"robustness":[104],"the":[106,115],"code,":[107],"automation":[109],"where":[110],"it":[111],"feasible":[113],"main":[116],"development":[117,124],"goals.":[118],"project":[120],"follows":[121],"an":[122],"open":[123],"model,":[125],"we":[127],"welcome":[128],"contributions.":[129]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":20},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":16},{"year":2016,"cited_by_count":7}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
