{"id":"https://openalex.org/W6921119902","doi":"https://doi.org/10.6094/unifr/240206","title":"Developing a workflow management system for fragment-based virtual screening","display_name":"Developing a workflow management system for fragment-based virtual screening","publication_year":2023,"publication_date":"2023-01-01","ids":{"openalex":"https://openalex.org/W6921119902","doi":"https://doi.org/10.6094/unifr/240206"},"language":"en","primary_location":{"id":"doi:10.6094/unifr/240206","is_oa":true,"landing_page_url":"https://doi.org/10.6094/unifr/240206","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"type":"other","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.6094/unifr/240206","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Bray, Simon A.","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Bray, Simon A.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8224999904632568},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5509999990463257},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5379999876022339},{"id":"https://openalex.org/keywords/service","display_name":"Service (business)","score":0.43529999256134033},{"id":"https://openalex.org/keywords/order","display_name":"Order (exchange)","score":0.40059998631477356},{"id":"https://openalex.org/keywords/substructure","display_name":"Substructure","score":0.37790000438690186},{"id":"https://openalex.org/keywords/workflow-management-system","display_name":"Workflow management system","score":0.358599990606308},{"id":"https://openalex.org/keywords/troubleshooting","display_name":"Troubleshooting","score":0.33629998564720154}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8224999904632568},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6987000107765198},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5509999990463257},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5379999876022339},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4650000035762787},{"id":"https://openalex.org/C2780378061","wikidata":"https://www.wikidata.org/wiki/Q25351891","display_name":"Service (business)","level":2,"score":0.43529999256134033},{"id":"https://openalex.org/C182306322","wikidata":"https://www.wikidata.org/wiki/Q1779371","display_name":"Order (exchange)","level":2,"score":0.40059998631477356},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.39989998936653137},{"id":"https://openalex.org/C99679407","wikidata":"https://www.wikidata.org/wiki/Q56761637","display_name":"Substructure","level":2,"score":0.37790000438690186},{"id":"https://openalex.org/C140824633","wikidata":"https://www.wikidata.org/wiki/Q2808660","display_name":"Workflow management system","level":3,"score":0.358599990606308},{"id":"https://openalex.org/C147494362","wikidata":"https://www.wikidata.org/wiki/Q2078905","display_name":"Troubleshooting","level":2,"score":0.33629998564720154},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.33500000834465027},{"id":"https://openalex.org/C149091818","wikidata":"https://www.wikidata.org/wiki/Q2429814","display_name":"Software system","level":3,"score":0.30649998784065247},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.295199990272522},{"id":"https://openalex.org/C19612761","wikidata":"https://www.wikidata.org/wiki/Q8034836","display_name":"Workflow technology","level":3,"score":0.28859999775886536},{"id":"https://openalex.org/C198783460","wikidata":"https://www.wikidata.org/wiki/Q629173","display_name":"Management system","level":2,"score":0.28769999742507935},{"id":"https://openalex.org/C188220564","wikidata":"https://www.wikidata.org/wiki/Q3325097","display_name":"Workflow engine","level":3,"score":0.28519999980926514},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.2849000096321106},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.28369998931884766},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.2800000011920929},{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.2793999910354614},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.2736999988555908},{"id":"https://openalex.org/C180198813","wikidata":"https://www.wikidata.org/wiki/Q121182","display_name":"Information system","level":2,"score":0.25839999318122864},{"id":"https://openalex.org/C116537","wikidata":"https://www.wikidata.org/wiki/Q2169973","display_name":"Service provider","level":3,"score":0.2572999894618988}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.6094/unifr/240206","is_oa":true,"landing_page_url":"https://doi.org/10.6094/unifr/240206","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.6094/unifr/240206","is_oa":true,"landing_page_url":"https://doi.org/10.6094/unifr/240206","pdf_url":null,"source":{"id":"https://openalex.org/S4306401057","display_name":"FreiDok plus (Universit\u00e4tsbibliothek Freiburg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I161046081","host_organization_name":"University of Freiburg","host_organization_lineage":["https://openalex.org/I161046081"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[{"score":0.4566049873828888,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Drug":[0],"development":[1],"is":[2,22,32,80,95,104,155,216,333,343,479,575,586,608],"a":[3,37,77,85,98,102,105,113,116,149,157,244,257,272,322,329,346,395,406,448,468,480,549,568,576,590,638,662,702,773,779,789],"long,":[4],"complex":[5,302,484,560],"and":[6,35,62,131,208,213,229,236,294,368,389,417,510,546,585,603,613,621,645,682,687,732,744,753,776,808,821],"expensive":[7],"process.":[8],"In":[9,345,493,527],"particular,":[10],"the":[11,39,50,139,161,168,192,223,238,240,268,277,284,292,326,334,358,362,371,384,403,409,421,428,456,474,477,497,500,522,531,534,543,554,564,597,601,604,611,622,635,647,659,679,685,708,715,719,759,793],"first":[12],"step":[13],"of":[14,19,41,52,93,141,151,179,210,279,287,319,328,375,386,394,405,411,420,442,499,533,600,637,641,649,652,661,678,689,691,710,714,718,778],"obtaining":[15],"an":[16,90,126,650,675],"initial":[17,91],"list":[18,92,150],"drug":[20,118],"candidates":[21,94,165],"challenging.":[23],"Experimental":[24],"screening,":[25],"for":[26,115,317,431,450,483,571,581,592,610,782],"example":[27],"using":[28,542,563],"protein-ligand":[29,60,740],"binding":[30,734,795,803],"assays,":[31],"fundamentally":[33],"limited,":[34],"as":[36,57,112,198,200,226,314,567,589],"result,":[38],"concept":[40],"virtual":[42,341,390,452,703],"screening":[43,48,342,453,619,704],"comes":[44],"into":[45,256],"play.":[46],"Virtual":[47],"involves":[49],"use":[51,243,327,393,498,660],"in":[53,72,124,145,181,201,340,383,559,617,643],"silico":[54],"experiments":[55,364],"such":[56,313],"statistical":[58],"analyses,":[59],"docking,":[61,741],"free":[63,582],"energy":[64,583],"calculations":[65,743],"based":[66,454,726],"on":[67,191,455,553,727,792,805],"molecular":[68],"dynamics":[69],"(MD)":[70],"simulation,":[71],"order":[73,146,494,528],"to":[74,82,84,147,159,167,219,231,253,355,401,426,436,446,495,508,519,529,596,670,683,698,799],"predict":[75],"whether":[76],"particular":[78,86,813],"compound":[79,108],"likely":[81],"bind":[83,166],"target":[87,169,324],"protein.":[88,170],"Often,":[89],"generated":[96,725],"by":[97,138,360,739,755,769,772],"fragment-":[99],"approach,":[100],"where":[101],"fragment":[103,593,761],"small":[106,598],"organic":[107],"that":[109,163,176,304,488,515,624,812],"can":[110,121,132,177,242,261,264,463],"serve":[111],"substructure":[114],"putative":[117],"candidate.":[119],"Fragments":[120],"be":[122,134,178,254,263,265,353,464],"found":[123,798],"either":[125,466],"experimental":[127,699,756],"or":[128,136,271,365,472,486],"theoretical":[129],"manner,":[130],"then":[133,156,230,262,767],"combined,":[135],"amended":[137],"addition":[140],"other":[142,293,350,432],"functional":[143],"groups,":[144],"produce":[148],"candidate":[152],"molecules.":[153],"There":[154,171],"need":[158],"determine":[160],"likelihood":[162],"these":[164,184],"are":[172,186,194,424],"several":[173,306,690],"computer-based":[174],"methods":[175,185],"service":[180],"this":[182,443],"task;":[183],"not":[187],"mutually":[188],"exclusive,":[189],"but":[190],"contrary":[193],"typically":[195],"used":[196,465,578,616],"sequentially":[197,738],"well":[199],"parallel.":[202],"However,":[203],"they":[204],"require":[205,305,490],"different":[206,307],"amounts":[207],"types":[209],"computational":[211,387],"resources,":[212,221],"careful":[214],"planning":[215],"therefore":[217],"required":[218],"manage":[220],"organise":[222,235],"software":[224,308],"tools":[225,252,289,309,413,545],"complete":[227],"workflows,":[228],"deploy":[232],"them.":[233],"To":[234],"perform":[237],"analysis,":[239],"scientist":[241],"workflow":[245,330,396,458,663,781],"management":[246,331,397,459,664],"system.":[247,460,665],"Such":[248],"systems":[249],"allow":[250,516],"multiple":[251,672],"concatenated":[255],"single":[258,323],"pipeline,":[259],"which":[260,607,656,787],"executed":[266],"via":[267,521],"command":[269,501],"line":[270,502],"graphical":[273,469],"interface.":[274],"This":[275,461],"has":[276,377],"advantage":[278],"being":[280],"more":[281],"convenient":[282],"than":[283],"tedious":[285],"execution":[286,636,777],"individual":[288],"one":[290],"after":[291],"helps":[295,400],"avoid":[296],"any":[297],"manual":[298],"errors.":[299],"For":[300],"highly":[301],"analyses":[303,429,487],"with":[310,415,561,707,818],"stepwise":[311],"repetition,":[312],"MD":[315,631],"simulations":[316,366,485],"hundreds":[318],"ligands":[320],"against":[321,758],"protein,":[325],"system":[332,399,570,580],"only":[335],"viable":[336],"option.":[337],"Another":[338],"challenge":[339],"reproducibility.":[344],"reproducible":[347],"scientific":[348],"work,":[349],"scientists":[351,433],"must":[352],"able":[354,669],"critically":[356],"evaluate":[357],"work":[359,444],"performing":[361],"same":[363],"themselves":[367],"thus":[369],"verifying":[370],"results.":[372],"The":[373,392,440,666,693],"issue":[374],"reproducibility":[376,404],"received":[378],"much":[379],"attention":[380],"recently,":[381],"including":[382],"field":[385],"chemistry":[388],"screening.":[391],"ix":[398],"increase":[402],"study,":[407],"because":[408],"details":[410],"all":[412,418],"run,":[414],"parameters":[416],"versions":[419],"tool":[422],"software,":[423],"recorded":[425],"make":[427,496],"repeatable":[430],"who":[434],"want":[435],"verify":[437],"their":[438,733],"work.":[439],"focus":[441],"was":[445,551,668,705,736,797,810],"develop":[447],"platform":[449,462,535],"fragment-based":[451,618],"Galaxy":[457,520],"through":[467,473],"web-based":[470],"interface":[471],"command-line":[475],"-":[476],"latter":[478],"useful":[481,588],"alternative":[482],"may":[489],"additional":[491],"scripting.":[492],"easier,":[503],"significant":[504],"contributions":[505],"were":[506,539,696,724,751,766],"made":[507],"Planemo":[509],"BioBlend,":[511],"two":[512,537],"Python":[513],"libraries":[514],"direct":[517],"access":[518],"Application":[523],"programming":[524],"Interface":[525],"(API).":[526],"demonstrate":[530],"utility":[532],"developed,":[536],"projects":[538],"carried":[540],"out":[541],"developed":[544],"workflows.":[547],"First,":[548],"study":[550],"performed":[552,706],"T4":[555],"lysozyme":[556],"mutant":[557],"L99A":[558],"benzene":[562,605,625],"dcTMD":[565,633,680,745,780,822],"technique":[566],"model":[569,579,591],"fragment-protein":[572],"binding.":[573],"T4L-L99A":[574],"commonly":[577],"calculations,":[584],"especially":[587,816],"binding,":[594],"due":[595],"size":[599],"pocket":[602],"ligand,":[606],"typical":[609],"compounds":[612,723,765],"pockets":[614],"generally":[615],"studies,":[620],"fact":[623],"binds":[626],"rather":[627],"weakly.":[628],"Like":[629],"many":[630],"methods,":[632],"requires":[634,646],"large":[639],"number":[640],"steps":[642],"sequence,":[644],"creation":[648],"ensemble":[651],"simulations,":[653],"both":[654,819],"features":[655],"benefit":[657],"from":[658],"analysis":[667],"uncover":[671],"unbinding":[673],"pathways,":[674],"essential":[676],"feature":[677],"method,":[681],"characterise":[684],"thermodynamics":[686],"kinetics":[688],"these.":[692],"final":[694],"results":[695],"comparable":[697],"benchmarks.":[700],"Second,":[701],"aim":[709],"identifying":[711],"effective":[712],"inhibitors":[713],"major":[716],"protease":[717],"SARS-CoV":[720],"virus;":[721],"53,000":[722],"22":[728],"non-covalent":[729],"crystallographic":[730,760],"fragments,":[731],"ability":[735,804],"analysed":[737],"MMGBSA":[742,820],"simulations.":[746],"Several":[747],"million":[748],"docking":[749],"poses":[750],"generated,":[752],"scored":[754],"validation":[757],"structures.":[762],"Over":[763],"200":[764],"assessed":[768],"MMGBSA,":[770],"followed":[771],"further":[774],"filtering":[775],"50":[783],"compounds.":[784],"One":[785],"fragment,":[786],"enforces":[788],"conformational":[790],"change":[791],"protein":[794],"site,":[796],"confer":[800],"particularly":[801],"strong":[802],"derived":[806],"compounds,":[807],"it":[809],"shown":[811],"interactions":[814],"correlated":[815],"strongly":[817],"scores.":[823]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2025-10-10T00:00:00"}
