{"id":"https://openalex.org/W4410227893","doi":"https://doi.org/10.1371/journal.pcbi.1013030","title":"Ten quick tips to perform meaningful and reproducible molecular docking calculations","display_name":"Ten quick tips to perform meaningful and reproducible molecular docking calculations","publication_year":2025,"publication_date":"2025-05-09","ids":{"openalex":"https://openalex.org/W4410227893","doi":"https://doi.org/10.1371/journal.pcbi.1013030","pmid":"https://pubmed.ncbi.nlm.nih.gov/40344147"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013030","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013030","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013030","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084513531","display_name":"Elvis A. F. Martis","orcid":"https://orcid.org/0000-0002-4919-6847"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4387154840","display_name":"Unit\u00e9 en Sciences Biologiques et Biotechnologies de Nantes","ror":"https://ror.org/05ef4v550","country_code":null,"type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4387154840","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I97188460","display_name":"Nantes Universit\u00e9","ror":"https://ror.org/03gnr7b55","country_code":"FR","type":"education","lineage":["https://openalex.org/I97188460"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Elvis A. F. Martis","raw_affiliation_strings":["Nantes Universit\u00e9, CNRS, US2B, UMR 6286, Nantes, France"],"raw_orcid":"https://orcid.org/0000-0002-4919-6847","affiliations":[{"raw_affiliation_string":"Nantes Universit\u00e9, CNRS, US2B, UMR 6286, Nantes, France","institution_ids":["https://openalex.org/I4387154840","https://openalex.org/I97188460","https://openalex.org/I1294671590"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031008010","display_name":"St\u00e9phane T\u00e9l\u00e9tch\u00e9a","orcid":"https://orcid.org/0000-0002-2402-028X"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4387154840","display_name":"Unit\u00e9 en Sciences Biologiques et Biotechnologies de Nantes","ror":"https://ror.org/05ef4v550","country_code":null,"type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I4387154840","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I97188460","display_name":"Nantes Universit\u00e9","ror":"https://ror.org/03gnr7b55","country_code":"FR","type":"education","lineage":["https://openalex.org/I97188460"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"St\u00e9phane T\u00e9letch\u00e9a","raw_affiliation_strings":["Nantes Universit\u00e9, CNRS, US2B, UMR 6286, Nantes, France"],"raw_orcid":"https://orcid.org/0000-0002-2402-028X","affiliations":[{"raw_affiliation_string":"Nantes Universit\u00e9, CNRS, US2B, UMR 6286, Nantes, France","institution_ids":["https://openalex.org/I4387154840","https://openalex.org/I97188460","https://openalex.org/I1294671590"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":19.6368,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.99377952,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"21","issue":"5","first_page":"e1013030","last_page":"e1013030"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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/T11440","display_name":"Click Chemistry and Applications","score":0.9855999946594238,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9639999866485596,"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":0.8037895560264587},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6240373849868774},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.5518954396247864},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4280087947845459},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.30323952436447144},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.298225462436676},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.2545982003211975},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.19081461429595947},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11209839582443237}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8037895560264587},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6240373849868774},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.5518954396247864},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4280087947845459},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.30323952436447144},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.298225462436676},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.2545982003211975},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.19081461429595947},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11209839582443237},{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1371/journal.pcbi.1013030","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013030","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40344147","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40344147","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1013030","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1013030","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013030","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013030","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3185549539","display_name":null,"funder_award_id":"ANR-22-CE18-0015-03","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":74,"referenced_works":["https://openalex.org/W1512801428","https://openalex.org/W1558188591","https://openalex.org/W1757990252","https://openalex.org/W1971698657","https://openalex.org/W1978809115","https://openalex.org/W1985588649","https://openalex.org/W1986982278","https://openalex.org/W1995089537","https://openalex.org/W1998380792","https://openalex.org/W1999022189","https://openalex.org/W2001586003","https://openalex.org/W2013848575","https://openalex.org/W2017663720","https://openalex.org/W2021534482","https://openalex.org/W2024331611","https://openalex.org/W2025816743","https://openalex.org/W2027423337","https://openalex.org/W2027976675","https://openalex.org/W2031194866","https://openalex.org/W2042572511","https://openalex.org/W2043509228","https://openalex.org/W2049752908","https://openalex.org/W2050456292","https://openalex.org/W2059371854","https://openalex.org/W2069152576","https://openalex.org/W2074473216","https://openalex.org/W2079953901","https://openalex.org/W2091734240","https://openalex.org/W2095719702","https://openalex.org/W2100947872","https://openalex.org/W2108001390","https://openalex.org/W2112411768","https://openalex.org/W2114779636","https://openalex.org/W2127760066","https://openalex.org/W2132629607","https://openalex.org/W2144659448","https://openalex.org/W2145355174","https://openalex.org/W2151919617","https://openalex.org/W2158534713","https://openalex.org/W2164088236","https://openalex.org/W2302501749","https://openalex.org/W2567231876","https://openalex.org/W2606044016","https://openalex.org/W2609454166","https://openalex.org/W2743456491","https://openalex.org/W2752184939","https://openalex.org/W2769496043","https://openalex.org/W2774836366","https://openalex.org/W2888400067","https://openalex.org/W2898210859","https://openalex.org/W2920724574","https://openalex.org/W2922133186","https://openalex.org/W2943893168","https://openalex.org/W2970628659","https://openalex.org/W2983453316","https://openalex.org/W3007329471","https://openalex.org/W3146157593","https://openalex.org/W3177828909","https://openalex.org/W3201539868","https://openalex.org/W3203999935","https://openalex.org/W4242372416","https://openalex.org/W4309413039","https://openalex.org/W4362677501","https://openalex.org/W4362720950","https://openalex.org/W4392526270","https://openalex.org/W4392544734","https://openalex.org/W4393991916","https://openalex.org/W4394014753","https://openalex.org/W4394688967","https://openalex.org/W4397042806","https://openalex.org/W4398222167","https://openalex.org/W4403605221","https://openalex.org/W4403922670","https://openalex.org/W7014944705"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W1581147483","https://openalex.org/W4310018788","https://openalex.org/W4398796548","https://openalex.org/W2329052364","https://openalex.org/W2162967120","https://openalex.org/W1567411871","https://openalex.org/W2553094381"],"abstract_inverted_index":{"Molecular":[0],"docking":[1,40,59,84,99],"is":[2,22,69],"a":[3,28],"useful":[4],"method":[5],"for":[6,85],"predicting":[7],"the":[8,62,72],"binding":[9],"affinity":[10],"and":[11,46,94,104],"conformation":[12],"of":[13,61],"small":[14],"chemical":[15,30,35],"entities":[16],"to":[17,25,32,57,70,77,90,100],"support":[18],"lead":[19],"optimisation.":[20],"It":[21],"also":[23],"used":[24],"virtually":[26],"screen":[27],"large":[29],"database":[31],"find":[33],"new":[34],"entities.":[36],"There":[37],"are":[38],"several":[39],"programs":[41],"available":[42],"with":[43,74],"different":[44],"algorithms":[45],"varying":[47],"preparation":[48],"steps.":[49],"We":[50,88],"identify":[51],"ten":[52],"quick":[53],"tips":[54],"that":[55,92],"apply":[56],"molecular":[58,83,98],"irrespective":[60],"program":[63],"one":[64],"might":[65],"choose.":[66],"Our":[67],"objective":[68],"provide":[71],"beginners":[73,95],"important":[75],"things":[76],"keep":[78],"in":[79],"mind":[80],"while":[81],"using":[82],"their":[86],"research.":[87],"aim":[89],"ensure":[91],"experts":[93],"can":[96],"perform":[97],"yield":[101],"biologically":[102],"relevant":[103],"reproducible":[105],"results.":[106]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":6}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
