{"id":"https://openalex.org/W2941138866","doi":"https://doi.org/10.1186/s13321-019-0348-5","title":"QligFEP: an automated workflow for small molecule free energy calculations in Q","display_name":"QligFEP: an automated workflow for small molecule free energy calculations in Q","publication_year":2019,"publication_date":"2019-04-02","ids":{"openalex":"https://openalex.org/W2941138866","doi":"https://doi.org/10.1186/s13321-019-0348-5","mag":"2941138866","pmid":"https://pubmed.ncbi.nlm.nih.gov/30941533"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-019-0348-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0348-5","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0348-5","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/s13321-019-0348-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063810062","display_name":"Willem Jespers","orcid":"https://orcid.org/0000-0002-4951-9220"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Willem Jespers","raw_affiliation_strings":["Department of Cell and Molecular Biology, Uppsala University, Uppsala, 75124, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-4951-9220","affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, Uppsala University, Uppsala, 75124, Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057678554","display_name":"Mauricio Esguerra","orcid":"https://orcid.org/0000-0002-1775-586X"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Mauricio Esguerra","raw_affiliation_strings":["Department of Cell and Molecular Biology, Uppsala University, Uppsala, 75124, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-1775-586X","affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, Uppsala University, Uppsala, 75124, Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055674495","display_name":"Johan \u00c5qvist","orcid":"https://orcid.org/0000-0003-2091-0610"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Johan \u00c5qvist","raw_affiliation_strings":["Department of Cell and Molecular Biology, Uppsala University, Uppsala, 75124, Sweden"],"raw_orcid":"https://orcid.org/0000-0003-2091-0610","affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, Uppsala University, Uppsala, 75124, Sweden","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005325174","display_name":"Hugo Guti\u00e9rrez\u2010de\u2010Ter\u00e1n","orcid":"https://orcid.org/0000-0003-0459-3491"},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I2800139495","display_name":"Science for Life Laboratory","ror":"https://ror.org/04ev03g22","country_code":"SE","type":"facility","lineage":["https://openalex.org/I2800139495"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Hugo Guti\u00e9rrez-de-Ter\u00e1n","raw_affiliation_strings":["Department of Cell and Molecular Biology, Uppsala University, Uppsala, 75124, Sweden. hugo.gutierrez@icm.uu.se","Science for Life Laboratory, Uppsala University, Uppsala, Sweden. hugo.gutierrez@icm.uu.se","Science for Life Laboratory, Uppsala University, Uppsala, Sweden"],"raw_orcid":"https://orcid.org/0000-0003-0459-3491","affiliations":[{"raw_affiliation_string":"Department of Cell and Molecular Biology, Uppsala University, Uppsala, 75124, Sweden. hugo.gutierrez@icm.uu.se","institution_ids":["https://openalex.org/I123387679"]},{"raw_affiliation_string":"Science for Life Laboratory, Uppsala University, Uppsala, Sweden. hugo.gutierrez@icm.uu.se","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I123387679"]},{"raw_affiliation_string":"Science for Life Laboratory, Uppsala University, Uppsala, Sweden","institution_ids":["https://openalex.org/I2800139495","https://openalex.org/I123387679"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5005325174"],"corresponding_institution_ids":["https://openalex.org/I123387679","https://openalex.org/I2800139495"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":4.1415,"has_fulltext":true,"cited_by_count":88,"citation_normalized_percentile":{"value":0.95128293,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"11","issue":"1","first_page":"26","last_page":"26"},"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/T11162","display_name":"Enzyme Structure and Function","score":0.9968000054359436,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9945999979972839,"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/workflow","display_name":"Workflow","score":0.7766530513763428},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6356022357940674},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.4860551655292511},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4207462668418884},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3408868610858917},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.23682516813278198},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10509401559829712},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.07163727283477783}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7766530513763428},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6356022357940674},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.4860551655292511},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4207462668418884},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3408868610858917},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.23682516813278198},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10509401559829712},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.07163727283477783}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13321-019-0348-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0348-5","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0348-5","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:30941533","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30941533","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:DiVA.org:uu-382389","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-382389","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:0fdb0109a1ba4d81a05fe86958fbb923","is_oa":false,"landing_page_url":"https://doaj.org/article/0fdb0109a1ba4d81a05fe86958fbb923","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 11, Iss 1, Pp 1-16 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5443577","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6444553","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/s13321-019-0348-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0348-5","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0348-5","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":[{"score":0.8999999761581421,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2941138866.pdf","grobid_xml":"https://content.openalex.org/works/W2941138866.grobid-xml"},"referenced_works_count":75,"referenced_works":["https://openalex.org/W120961229","https://openalex.org/W404240460","https://openalex.org/W1625910593","https://openalex.org/W1672217021","https://openalex.org/W1970973025","https://openalex.org/W1974167806","https://openalex.org/W1975353473","https://openalex.org/W1982680156","https://openalex.org/W1989195611","https://openalex.org/W1992100298","https://openalex.org/W1992156271","https://openalex.org/W1997119191","https://openalex.org/W1999248820","https://openalex.org/W2004124673","https://openalex.org/W2011207690","https://openalex.org/W2013979082","https://openalex.org/W2014060139","https://openalex.org/W2015688756","https://openalex.org/W2021518677","https://openalex.org/W2023400093","https://openalex.org/W2023818227","https://openalex.org/W2027987013","https://openalex.org/W2031101869","https://openalex.org/W2031168104","https://openalex.org/W2039399096","https://openalex.org/W2043383571","https://openalex.org/W2044656372","https://openalex.org/W2047631698","https://openalex.org/W2070753604","https://openalex.org/W2075468840","https://openalex.org/W2081775931","https://openalex.org/W2093755925","https://openalex.org/W2100112706","https://openalex.org/W2101234009","https://openalex.org/W2104630281","https://openalex.org/W2106140689","https://openalex.org/W2109154308","https://openalex.org/W2118958548","https://openalex.org/W2131643298","https://openalex.org/W2132280554","https://openalex.org/W2133641393","https://openalex.org/W2135732933","https://openalex.org/W2139272370","https://openalex.org/W2139447954","https://openalex.org/W2140151763","https://openalex.org/W2144288821","https://openalex.org/W2147993766","https://openalex.org/W2148911913","https://openalex.org/W2154670681","https://openalex.org/W2155554859","https://openalex.org/W2159367911","https://openalex.org/W2167068661","https://openalex.org/W2222589778","https://openalex.org/W2323942455","https://openalex.org/W2337120805","https://openalex.org/W2359290780","https://openalex.org/W2402625670","https://openalex.org/W2404280981","https://openalex.org/W2420659973","https://openalex.org/W2463492870","https://openalex.org/W2479221391","https://openalex.org/W2511847589","https://openalex.org/W2552522590","https://openalex.org/W2589948472","https://openalex.org/W2603333707","https://openalex.org/W2606142660","https://openalex.org/W2617367274","https://openalex.org/W2744485267","https://openalex.org/W2749873612","https://openalex.org/W2772606519","https://openalex.org/W2774484667","https://openalex.org/W2792098984","https://openalex.org/W2996669101","https://openalex.org/W4230274588","https://openalex.org/W4248107770"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W188202134"],"abstract_inverted_index":{"The":[0],"process":[1],"of":[2,22,30,38,51,57,66,79,84,122,124,193,203,215,221,265,285],"ligand":[3],"binding":[4,40,184,253],"to":[5,72,100,134,169,188,250],"a":[6,62,98,112,201,219,263],"biological":[7],"target":[8],"can":[9,166],"be":[10,135,167],"represented":[11],"as":[12,35,180,182],"the":[13,16,23,28,36,48,55,73,76,85,91,119,125,130,141,146,152,156,183,189,212,229,252,273,281],"equilibrium":[14],"between":[15,88,155,255],"relevant":[17],"solvated":[18],"and":[19,54,218,278,290],"bound":[20],"states":[21],"ligand.":[24],"This":[25,197],"which":[26,129,259],"is":[27,68,133,198,270],"basis":[29],"structure-based,":[31],"rigorous":[32],"methods":[33],"such":[34],"estimation":[37],"relative":[39,131],"affinities":[41,254],"by":[42],"free":[43,173],"energy":[44],"perturbation":[45,153],"(FEP).":[46],"Despite":[47],"growing":[49],"capacity":[50],"computing":[52],"power":[53],"development":[56],"more":[58],"accurate":[59],"force":[60,286],"fields,":[61],"high":[63],"throughput":[64],"application":[65],"FEP":[67,108,149,209],"currently":[69],"hampered":[70],"due":[71,187],"need,":[74],"in":[75,90,140,200,211,235,272],"current":[77],"schemes,":[78],"an":[80,104],"expert":[81],"user":[82],"definition":[83],"\u201calchemical\u201d":[86],"transformations":[87],"molecules":[89],"series":[92,220,264],"explored.":[93],"Here,":[94],"we":[95,260],"present":[96,139],"QligFEP,":[97],"solution":[99],"this":[101,117,163],"problem":[102],"using":[103],"automated":[105],"workflow":[106],"for":[107,128,175,246],"calculations":[109],"based":[110],"on":[111],"dual":[113],"topology":[114],"approach.":[115],"In":[116,241],"scheme,":[118],"starting":[120],"poses":[121],"each":[123],"two":[126,157],"ligands,":[127],"affinity":[132,185],"calculated,":[136],"are":[137,234],"explicitly":[138],"MD":[142,275],"simulations":[143],"associated":[144],"with":[145,232,238,262,280],"(dual":[147],"topology)":[148],"transformation,":[150],"making":[151],"pathway":[154],"ligands":[158],"univocal.":[159],"We":[160],"show":[161],"that":[162],"generalized":[164],"method":[165],"applied":[168],"accurately":[170],"estimate":[171],"solvation":[172],"energies":[174],"amino":[176],"acid":[177],"sidechain":[178],"mimics,":[179],"well":[181],"shifts":[186],"chemical":[190],"changes":[191],"typical":[192],"lead":[194],"optimization":[195],"processes.":[196],"illustrated":[199],"number":[202],"protein":[204],"systems":[205],"extracted":[206],"from":[207],"other":[208],"studies":[210],"literature:":[213],"inhibitors":[214],"CDK2":[216],"kinase":[217,267],"A2A":[222],"adenosine":[223],"G":[224],"protein-coupled":[225],"receptor":[226],"antagonists,":[227],"where":[228],"results":[230],"obtained":[231],"QligFEP":[233,269],"excellent":[236],"agreement":[237],"experimental":[239],"data.":[240],"addition,":[242],"our":[243],"protocol":[244],"allows":[245],"scaffold":[247],"hopping":[248],"perturbations":[249],"identify":[251],"different":[256],"core":[257],"scaffolds,":[258],"illustrate":[261],"Chk1":[266],"inhibitors.":[268],"implemented":[271],"open-source":[274],"package":[276],"Q,":[277],"works":[279],"most":[282],"common":[283],"family":[284],"fields:":[287],"OPLS,":[288],"CHARMM":[289],"AMBER.":[291]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":19},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
