{"id":"https://openalex.org/W3024252757","doi":"https://doi.org/10.1093/bioinformatics/btaa481","title":"PLIDflow: an open-source workflow for the online analysis of protein\u2013ligand docking using galaxy","display_name":"PLIDflow: an open-source workflow for the online analysis of protein\u2013ligand docking using galaxy","publication_year":2020,"publication_date":"2020-05-12","ids":{"openalex":"https://openalex.org/W3024252757","doi":"https://doi.org/10.1093/bioinformatics/btaa481","mag":"3024252757","pmid":"https://pubmed.ncbi.nlm.nih.gov/32415960"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa481","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa481","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/14/4203/34306801/btaa481.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/14/4203/34306801/btaa481.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019445326","display_name":"Eugenia Ulzurrun","orcid":null},"institutions":[{"id":"https://openalex.org/I4210164724","display_name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga","ror":"https://ror.org/05n3asa33","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210164724"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Eugenia Ulzurrun","raw_affiliation_strings":["Department of Computer Architecture , Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga-IBIMA, University of M\u00e1laga, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Architecture , Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga-IBIMA, University of M\u00e1laga, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I4210164724","https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023236269","display_name":"Yorley Duarte","orcid":"https://orcid.org/0000-0002-8127-7540"},"institutions":[{"id":"https://openalex.org/I13897259","display_name":"Universidad Andr\u00e9s Bello","ror":"https://ror.org/01qq57711","country_code":"CL","type":"education","lineage":["https://openalex.org/I13897259"]}],"countries":["CL"],"is_corresponding":false,"raw_author_name":"Yorley Duarte","raw_affiliation_strings":["Center for Bioinformatics and Integrative Biology , Facultad de Ciencias de la Vida, Universidad Andr\u00e9s Bello, Santiago, Chile"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Integrative Biology , Facultad de Ciencias de la Vida, Universidad Andr\u00e9s Bello, Santiago, Chile","institution_ids":["https://openalex.org/I13897259"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013154759","display_name":"Esteban P\u00e9rez-Wohlfeil","orcid":"https://orcid.org/0000-0002-3572-686X"},"institutions":[{"id":"https://openalex.org/I4210164724","display_name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga","ror":"https://ror.org/05n3asa33","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210164724"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Esteban Perez-Wohlfeil","raw_affiliation_strings":["Department of Computer Architecture , Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga-IBIMA, University of M\u00e1laga, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Architecture , Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga-IBIMA, University of M\u00e1laga, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I4210164724","https://openalex.org/I82767444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013850089","display_name":"Fernando D. Gonz\u00e1lez\u2010Nilo","orcid":"https://orcid.org/0000-0001-6857-3575"},"institutions":[{"id":"https://openalex.org/I13897259","display_name":"Universidad Andr\u00e9s Bello","ror":"https://ror.org/01qq57711","country_code":"CL","type":"education","lineage":["https://openalex.org/I13897259"]}],"countries":["CL"],"is_corresponding":false,"raw_author_name":"Fernando Gonzalez-Nilo","raw_affiliation_strings":["Center for Bioinformatics and Integrative Biology , Facultad de Ciencias de la Vida, Universidad Andr\u00e9s Bello, Santiago, Chile"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Integrative Biology , Facultad de Ciencias de la Vida, Universidad Andr\u00e9s Bello, Santiago, Chile","institution_ids":["https://openalex.org/I13897259"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082510742","display_name":"Oswaldo Trelles","orcid":"https://orcid.org/0000-0003-1554-8987"},"institutions":[{"id":"https://openalex.org/I4210164724","display_name":"Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga","ror":"https://ror.org/05n3asa33","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210164724"]},{"id":"https://openalex.org/I82767444","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28","country_code":"ES","type":"education","lineage":["https://openalex.org/I82767444"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Oswaldo Trelles","raw_affiliation_strings":["Department of Computer Architecture , Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga-IBIMA, University of M\u00e1laga, M\u00e1laga, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Architecture , Instituto de Investigaci\u00f3n Biom\u00e9dica de M\u00e1laga-IBIMA, University of M\u00e1laga, M\u00e1laga, Spain","institution_ids":["https://openalex.org/I4210164724","https://openalex.org/I82767444"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5019445326"],"corresponding_institution_ids":["https://openalex.org/I4210164724","https://openalex.org/I82767444"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.2763,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.61130435,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"36","issue":"14","first_page":"4203","last_page":"4205"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.833299994468689,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.833299994468689,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.04899999871850014,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.01979999989271164,"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/docking","display_name":"Docking (animal)","score":0.8086841106414795},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.6936926245689392},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.6860508918762207},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6763028502464294},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5943475365638733},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5938346982002258},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.4758313000202179},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47024479508399963},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3439633846282959},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2585294246673584},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2294750213623047},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18624693155288696},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.15263861417770386}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8086841106414795},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.6936926245689392},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6860508918762207},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6763028502464294},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5943475365638733},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5938346982002258},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.4758313000202179},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47024479508399963},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3439633846282959},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2585294246673584},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2294750213623047},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18624693155288696},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.15263861417770386},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa481","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa481","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/14/4203/34306801/btaa481.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32415960","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32415960","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa481","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa481","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/14/4203/34306801/btaa481.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320311265","display_name":"Universidad de M\u00e1laga","ror":"https://ror.org/036b2ww28"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1606947757","https://openalex.org/W1842005578","https://openalex.org/W1944603233","https://openalex.org/W1969761972","https://openalex.org/W2047399603","https://openalex.org/W2086279137","https://openalex.org/W2105668062","https://openalex.org/W2134967712","https://openalex.org/W2158534713","https://openalex.org/W2169678694","https://openalex.org/W2330799739","https://openalex.org/W2334483166","https://openalex.org/W2338719532","https://openalex.org/W2898599972","https://openalex.org/W2912890432","https://openalex.org/W2980497069","https://openalex.org/W4229880569","https://openalex.org/W4294141750"],"related_works":["https://openalex.org/W1581147483","https://openalex.org/W4310018788","https://openalex.org/W2329052364","https://openalex.org/W2059230675","https://openalex.org/W2376003823","https://openalex.org/W2057846043","https://openalex.org/W2336040088","https://openalex.org/W2027065525","https://openalex.org/W2773493604","https://openalex.org/W2269591907"],"abstract_inverted_index":{"MOTIVATION:":[0],"Molecular":[1],"docking":[2,24,40,63,172],"is":[3,51,77,178],"aimed":[4],"at":[5,190],"predicting":[6],"the":[7,48,66,127,130,135,138,145,152,163],"conformation":[8],"of":[9,42,47,68,91,129,137,144,162],"small-molecule":[10],"(ligands)":[11],"within":[12],"an":[13,26,115],"identified":[14],"binding":[15,140],"site":[16],"(BS)":[17],"in":[18,29,82,104,167],"a":[19,96,102],"target":[20],"protein":[21,36],"(receptor).":[22],"Protein-ligand":[23],"plays":[25],"important":[27],"role":[28],"modern":[30],"drug":[31],"discovery":[32],"and":[33,61,142],"biochemistry":[34],"for":[35,99],"engineering.":[37],"However,":[38],"efficient":[39],"analysis":[41],"proteins":[43],"requires":[44,65],"prior":[45],"knowledge":[46],"BS,":[49],"which":[50,57,71,124],"not":[52],"always":[53],"known.":[54],"The":[55,160],"process":[56,98,121],"covers":[58],"BS":[59],"identification":[60,128],"protein-ligand":[62,122],"usually":[64],"combination":[67],"different":[69],"programs,":[70],"require":[72],"several":[73],"input":[74],"parameters.":[75],"This":[76,147],"furtherly":[78],"aggravated":[79],"when":[80],"factoring":[81],"computational":[83,117],"demands,":[84],"such":[85],"as":[86],"CPU-time.":[87],"Therefore,":[88],"these":[89,110],"types":[90],"simulation":[92],"experiments":[93],"can":[94],"become":[95],"complex":[97],"researchers":[100],"without":[101],"background":[103],"computer":[105],"sciences.":[106],"RESULTS:":[107],"To":[108],"overcome":[109],"problems,":[111],"we":[112],"have":[113],"designed":[114],"automatic":[116],"workflow":[118],"(WF)":[119],"to":[120,134],"complexes,":[123],"runs":[125,150],"from":[126],"possible":[131],"BSs":[132],"positions":[133],"prediction":[136],"experimental":[139],"modes":[141],"affinities":[143],"ligand.":[146],"open-access":[148],"WF":[149],"under":[151],"Galaxy":[153],"platform":[154],"that":[155],"integrates":[156],"public":[157],"domain":[158],"software.":[159,173],"results":[161],"proposed":[164],"method":[165],"are":[166,188],"close":[168],"agreement":[169],"with":[170],"state-of-the-art":[171],"AVAILABILITY":[174],"AND":[175],"IMPLEMENTATION:":[176],"Software":[177],"available":[179,189],"at:":[180],"https://pistacho.ac.uma.es/galaxy-bitlab.":[181],"CONTACT:":[182],"euv@uma.es.":[183],"SUPPLEMENTARY":[184],"INFORMATION:":[185],"Supplementary":[186],"data":[187],"Bioinformatics":[191],"online.":[192]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
