{"id":"https://openalex.org/W3076540051","doi":"https://doi.org/10.1021/acs.jcim.0c00206","title":"BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations","display_name":"BRIDGE: An Open Platform for Reproducible High-Throughput Free Energy Simulations","publication_year":2020,"publication_date":"2020-08-18","ids":{"openalex":"https://openalex.org/W3076540051","doi":"https://doi.org/10.1021/acs.jcim.0c00206","mag":"3076540051","pmid":"https://pubmed.ncbi.nlm.nih.gov/32810405"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00206","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_indexed_in_scopus":true,"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":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://eprints.soton.ac.uk/444424/1/Main_ApplNote_BRIDGE_FE_JCIM_2020R3TC.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023668095","display_name":"Tharindu Senapathi","orcid":"https://orcid.org/0000-0002-3277-4022"},"institutions":[{"id":"https://openalex.org/I157614274","display_name":"University of Cape Town","ror":"https://ror.org/03p74gp79","country_code":"ZA","type":"funder","lineage":["https://openalex.org/I157614274"]}],"countries":["ZA"],"is_corresponding":false,"raw_author_name":"Tharindu Senapathi","raw_affiliation_strings":["Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa"],"affiliations":[{"raw_affiliation_string":"Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa","institution_ids":["https://openalex.org/I157614274"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045487219","display_name":"Miroslav Suruzhon","orcid":"https://orcid.org/0000-0002-6794-1679"},"institutions":[{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"funder","lineage":["https://openalex.org/I43439940"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Miroslav Suruzhon","raw_affiliation_strings":["School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom","institution_ids":["https://openalex.org/I43439940"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087764384","display_name":"Christopher B. Barnett","orcid":"https://orcid.org/0000-0002-1467-5741"},"institutions":[{"id":"https://openalex.org/I157614274","display_name":"University of Cape Town","ror":"https://ror.org/03p74gp79","country_code":"ZA","type":"funder","lineage":["https://openalex.org/I157614274"]}],"countries":["ZA"],"is_corresponding":false,"raw_author_name":"Christopher B. Barnett","raw_affiliation_strings":["Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa"],"affiliations":[{"raw_affiliation_string":"Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa","institution_ids":["https://openalex.org/I157614274"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067820273","display_name":"Jonathan W. Essex","orcid":"https://orcid.org/0000-0003-2639-2746"},"institutions":[{"id":"https://openalex.org/I43439940","display_name":"University of Southampton","ror":"https://ror.org/01ryk1543","country_code":"GB","type":"funder","lineage":["https://openalex.org/I43439940"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jonathan Essex","raw_affiliation_strings":["School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom","institution_ids":["https://openalex.org/I43439940"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006872896","display_name":"Kevin J. Naidoo","orcid":"https://orcid.org/0000-0002-9898-3708"},"institutions":[{"id":"https://openalex.org/I157614274","display_name":"University of Cape Town","ror":"https://ror.org/03p74gp79","country_code":"ZA","type":"funder","lineage":["https://openalex.org/I157614274"]}],"countries":["ZA"],"is_corresponding":true,"raw_author_name":"Kevin J. Naidoo","raw_affiliation_strings":["Institute of Infectious Disease and Molecular Medicine, Faculty of Health Science, University of Cape Town, Rondebosch 7701, South Africa","Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa"],"affiliations":[{"raw_affiliation_string":"Scientific Computing Research Unit and Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa","institution_ids":["https://openalex.org/I157614274"]},{"raw_affiliation_string":"Institute of Infectious Disease and Molecular Medicine, Faculty of Health Science, University of Cape Town, Rondebosch 7701, South Africa","institution_ids":["https://openalex.org/I157614274"]}]}],"institution_assertions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5006872896"],"corresponding_institution_ids":["https://openalex.org/I157614274"],"apc_list":null,"apc_paid":null,"fwci":1.027,"has_fulltext":true,"fulltext_origin":"pdf","cited_by_count":13,"citation_normalized_percentile":{"value":0.57258,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":89},"biblio":{"volume":"60","issue":"11","first_page":"5290","last_page":"5295"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.999,"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":0.999,"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":0.996,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9913,"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/software-portability","display_name":"Software portability","score":0.58006054},{"id":"https://openalex.org/keywords/porting","display_name":"Porting","score":0.4794311},{"id":"https://openalex.org/keywords/python","display_name":"Python","score":0.4529851}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7717197},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5887365},{"id":"https://openalex.org/C63000827","wikidata":"https://www.wikidata.org/wiki/Q3080428","display_name":"Software portability","level":2,"score":0.58006054},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.5563421},{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.4794311},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.46714398},{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.45890564},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.4529851},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.38589817},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.38155437},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.32860708},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.32577395}],"mesh":[{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00206","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_indexed_in_scopus":true,"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":null,"is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"https://eprints.soton.ac.uk/444424/1/Main_ApplNote_BRIDGE_FE_JCIM_2020R3TC.pdf","pdf_url":"https://eprints.soton.ac.uk/444424/1/Main_ApplNote_BRIDGE_FE_JCIM_2020R3TC.pdf","source":{"id":"https://openalex.org/S4306401020","display_name":"ePrints Soton (University of Southampton)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_indexed_in_scopus":false,"is_core":false,"host_organization":"https://openalex.org/I43439940","host_organization_name":"University of Southampton","host_organization_lineage":["https://openalex.org/I43439940"],"host_organization_lineage_names":["University of Southampton"],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32810405","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_indexed_in_scopus":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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://eprints.soton.ac.uk/444424/1/Main_ApplNote_BRIDGE_FE_JCIM_2020R3TC.pdf","pdf_url":"https://eprints.soton.ac.uk/444424/1/Main_ApplNote_BRIDGE_FE_JCIM_2020R3TC.pdf","source":{"id":"https://openalex.org/S4306401020","display_name":"ePrints Soton (University of Southampton)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_indexed_in_scopus":false,"is_core":false,"host_organization":"https://openalex.org/I43439940","host_organization_name":"University of Southampton","host_organization_lineage":["https://openalex.org/I43439940"],"host_organization_lineage_names":["University of Southampton"],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.83}],"grants":[{"funder":"https://openalex.org/F4320307770","funder_display_name":"AstraZeneca","award_id":null},{"funder":"https://openalex.org/F4320307773","funder_display_name":"GlaxoSmithKline","award_id":null},{"funder":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation","award_id":"449130"},{"funder":"https://openalex.org/F4320320672","funder_display_name":"South African Medical Research Council","award_id":null},{"funder":"https://openalex.org/F4320320691","funder_display_name":"Department of Science and Technology, Republic of South Africa","award_id":null},{"funder":"https://openalex.org/F4320324164","funder_display_name":"University of Cape Town","award_id":null},{"funder":"https://openalex.org/F4320326627","funder_display_name":"Syngenta International","award_id":null},{"funder":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council","award_id":"EP/L015722/1"}],"datasets":[],"versions":[],"referenced_works_count":30,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1969488773","https://openalex.org/W1989195611","https://openalex.org/W2004124673","https://openalex.org/W2021832765","https://openalex.org/W2033906450","https://openalex.org/W2034194940","https://openalex.org/W2043383571","https://openalex.org/W2055648985","https://openalex.org/W2063206968","https://openalex.org/W2114227821","https://openalex.org/W2132262459","https://openalex.org/W2132925790","https://openalex.org/W2136482257","https://openalex.org/W2144305967","https://openalex.org/W2147993766","https://openalex.org/W2149170824","https://openalex.org/W2151020862","https://openalex.org/W2154670681","https://openalex.org/W2321484219","https://openalex.org/W2404280981","https://openalex.org/W2508846984","https://openalex.org/W2914266147","https://openalex.org/W2914963377","https://openalex.org/W2917207851","https://openalex.org/W2949223833","https://openalex.org/W2949467224","https://openalex.org/W2950265636","https://openalex.org/W2990010612","https://openalex.org/W3008264752"],"related_works":["https://openalex.org/W4312942606","https://openalex.org/W3124707092","https://openalex.org/W3123383020","https://openalex.org/W2912579397","https://openalex.org/W28826848","https://openalex.org/W2375332572","https://openalex.org/W2373446736","https://openalex.org/W2166776054","https://openalex.org/W2152694830","https://openalex.org/W1820309981"],"abstract_inverted_index":{"Biomolecular":[0],"Reaction":[1],"and":[2,55,58,75,99,125,161,176,185,192,206,222,236,256],"Interaction":[3],"Dynamics":[4],"Global":[5],"Environment":[6],"(BRIDGE)":[7],"is":[8,33],"an":[9,19,201],"open-source":[10],"web":[11,50,157],"platform":[12,65],"developed":[13],"with":[14],"the":[15,22,36,62,72,141,172,212,223,263],"aim":[16],"to":[17,27,92,220,229,261],"provide":[18],"environment":[20],"for":[21,52,66,80,216],"design":[23],"of":[24,77,130,189,195,204,214,254,267],"reliable":[25],"methods":[26,79,116,205,258],"conduct":[28],"reproducible":[29],"biomolecular":[30],"simulations.":[31,82],"It":[32],"built":[34],"on":[35,48,154,241],"well-known":[37],"Galaxy":[38],"bioinformatics":[39],"platform.":[40,145],"Through":[41],"this,":[42],"BRIDGE":[43,198],"hosts":[44],"computational":[45,78],"chemistry":[46],"tools":[47,89],"public":[49,190],"servers":[51,158],"internet":[53],"use":[54,108],"provides":[56],"machine-":[57],"operating-system-independent":[59],"portability":[60],"using":[61,171],"Docker":[63,143],"container":[64,144],"local":[67],"use.":[68],"This":[69,210],"construction":[70],"improves":[71],"accessibility,":[73],"shareability,":[74],"reproducibility":[76],"molecular":[81],"Here":[83],"we":[84,163],"present":[85,111],"integrated":[86],"free":[87,96,102,112,265],"energy":[88,113],"(or":[90],"apps)":[91],"calculate":[93],"absolute":[94],"binding":[95,101,264],"energies":[97,103,266],"(ABFEs)":[98],"relative":[100],"(RBFEs),":[104],"as":[105,123],"illustrated":[106],"through":[107,181],"cases.":[109],"We":[110,238],"perturbation":[114],"(FEP)":[115],"contained":[117],"in":[118,140],"various":[119],"software":[120,133],"packages":[121],"such":[122],"GROMACS":[124],"YANK":[126],"that":[127,165,226],"are":[128,227,259],"independent":[129,193],"hardware":[131],"configuration,":[132],"libraries,":[134],"or":[135],"operating":[136],"systems":[137],"when":[138],"ported":[139],"Galaxy-BRIDGE":[142],"By":[146],"performing":[147],"cyclin-dependent":[148],"kinase":[149],"2":[150],"(CDK2)":[151],"FEP":[152],"calculations":[153],"geographically":[155],"dispersed":[156],"(in":[159],"Africa":[160],"Europe),":[162],"illustrate":[164,239],"large-scale":[166],"computations":[167],"can":[168],"be":[169],"performed":[170],"exact":[173],"same":[174],"codes":[175],"methodology":[177],"by":[178,234],"collaborating":[179],"groups":[180],"publicly":[182],"shared":[183],"protocols":[184],"workflows.":[186],"The":[187],"ease":[188],"sharing":[191],"reproduction":[194],"simulations":[196],"via":[197],"makes":[199,211],"possible":[200],"open":[202],"review":[203],"complete":[207],"simulation":[208],"protocols.":[209],"discovery":[213],"inhibitors":[215],"drug":[217,249],"targets":[218],"accessible":[219],"nonexperts":[221],"computer":[224],"experiments":[225],"used":[228,260],"arrive":[230],"at":[231],"leads":[232],"verifiable":[233],"experts":[235],"reviewers.":[237],"this":[240],"\u03b2-galactoside":[242],"\u03b1-2,3-sialyltransferase":[243],"I":[244],"(ST3Gal-I),":[245],"a":[246,252],"breast":[247],"cancer":[248],"target,":[250],"where":[251],"combination":[253],"RBFE":[255],"ABFE":[257],"compute":[262],"three":[268],"inhibitors.":[269]},"abstract_inverted_index_v3":null,"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W3076540051","counts_by_year":[{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":4}],"updated_date":"2025-02-21T15:48:21.799202","created_date":"2020-08-24"}