{"id":"https://openalex.org/W1205728809","doi":"https://doi.org/10.17877/de290r-11534","title":"A simple click by click protocol to perform docking","display_name":"A simple click by click protocol to perform docking","publication_year":2013,"publication_date":"2013-09-23","ids":{"openalex":"https://openalex.org/W1205728809","doi":"https://doi.org/10.17877/de290r-11534","mag":"1205728809","pmid":"https://pubmed.ncbi.nlm.nih.gov/26648810","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/4669947"},"language":"en","primary_location":{"id":"pmh:oai:www.excli.de:article/1196","doi":null,"is_oa":true,"landing_page_url":"https://www.excli.de/excli/article/view/1196","pdf_url":"https://www.excli.de/excli/article/view/1196/2657","source":{"id":"https://openalex.org/S39273986","display_name":"EXCLI journal","issn_l":"1611-2156","issn":["1611-2156"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","ddh","doaj","dongbi-c","jufo-1","ki-jl-1","norway-1","oarl","poland-100","russia-white-list-1"],"host_organization":"https://openalex.org/P4310313779","host_organization_name":"IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund","host_organization_lineage":["https://openalex.org/P4310313779"],"host_organization_lineage_names":["IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"1611-2156","raw_type":"info:eu-repo/semantics/article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.excli.de/excli/article/view/1196/2657","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023153969","display_name":"Syed Mohd Danish Rizvi","orcid":"https://orcid.org/0000-0002-3106-4707","observed_orcids":["https://orcid.org/0000-0002-3106-4707"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rizvi, Syed Mohd. Danish","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049727196","display_name":"Shazi Shakil","orcid":"https://orcid.org/0000-0003-4075-9153","observed_orcids":["https://orcid.org/0000-0003-4075-9153"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shakil, Shazi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5107833497","display_name":"Mohd Haneef","orcid":"https://orcid.org/0000-0001-7131-9498","observed_orcids":["https://orcid.org/0000-0001-7131-9498"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Haneef, Mohd.","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":1.3508,"has_fulltext":true,"cited_by_count":355,"citation_normalized_percentile":{"value":0.77463194,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":100},"biblio":{"volume":"12","issue":null,"first_page":"831","last_page":"57"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":9.999999747378752e-05,"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/T11908","display_name":"Protein Interaction Studies and Fluorescence Analysis","score":9.999999747378752e-05,"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/molecular-docking","display_name":"molecular docking","score":0.9580000042915344},{"id":"https://openalex.org/keywords/protein-ligand-binding","display_name":"protein-ligand binding","score":0.7960000038146973},{"id":"https://openalex.org/keywords/compound-screening","display_name":"compound screening","score":0.6200000047683716},{"id":"https://openalex.org/keywords/binding-affinity-prediction","display_name":"binding affinity prediction","score":0.8209999799728394}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.660500705242157},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.5217500925064087},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5206541419029236},{"id":"https://openalex.org/C69610077","wikidata":"https://www.wikidata.org/wiki/Q912270","display_name":"Click chemistry","level":2,"score":0.45403218269348145},{"id":"https://openalex.org/C2780385302","wikidata":"https://www.wikidata.org/wiki/Q367158","display_name":"Protocol (science)","level":3,"score":0.4405588209629059},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.11423924565315247},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11061719059944153},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.10320881009101868},{"id":"https://openalex.org/C204787440","wikidata":"https://www.wikidata.org/wiki/Q188504","display_name":"Alternative medicine","level":2,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":9,"locations":[{"id":"pmh:oai:www.excli.de:article/1196","doi":null,"is_oa":true,"landing_page_url":"https://www.excli.de/excli/article/view/1196","pdf_url":"https://www.excli.de/excli/article/view/1196/2657","source":{"id":"https://openalex.org/S39273986","display_name":"EXCLI journal","issn_l":"1611-2156","issn":["1611-2156"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","ddh","doaj","dongbi-c","jufo-1","ki-jl-1","norway-1","oarl","poland-100","russia-white-list-1"],"host_organization":"https://openalex.org/P4310313779","host_organization_name":"IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund","host_organization_lineage":["https://openalex.org/P4310313779"],"host_organization_lineage_names":["IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"1611-2156","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4669947","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4669947","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"EXCLI J","raw_type":"Text"},{"id":"pmid:26648810","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26648810","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,"listed_in":[],"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":"EXCLI journal","raw_type":"Journal Article"},{"id":"pmh:oai:eldorado.tu-dortmund.de:2003/32962","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/2003/32962","pdf_url":"http://eldorado.tu-dortmund.de/bitstreams/c7570a38-bd5b-4c6b-a993-8ac933bc1f8b/download","source":{"id":"https://openalex.org/S4306400811","display_name":"Technische Universit\u00e4t Dortmund Eldorado (Technische Universit\u00e4t Dortmund)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210148506","host_organization_name":"Erich-Brost-Institut","host_organization_lineage":["https://openalex.org/I4210148506"],"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":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.806.1385","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.806.1385","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/d9/57/EXCLI-12-831.PMC4669947.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.827.1985","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.827.1985","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://eldorado.tu-dortmund.de:443/bitstream/2003/32962/1/Shakil_23092013_proof.pdf","raw_type":"text"},{"id":"doi:10.17877/de290r-11534","doi":"https://doi.org/10.17877/de290r-11534","is_oa":true,"landing_page_url":"https://doi.org/10.17877/de290r-11534","pdf_url":null,"source":{"id":"https://openalex.org/S4306400811","display_name":"Technische Universit\u00e4t Dortmund Eldorado (Technische Universit\u00e4t Dortmund)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210148506","host_organization_name":"Erich-Brost-Institut","host_organization_lineage":["https://openalex.org/I4210148506"],"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":"article-journal"},{"id":"mag:1205728809","doi":null,"is_oa":false,"landing_page_url":"https://eldorado.tu-dortmund.de/bitstream/2003/32962/1/Shakil_23092013_proof.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"mag:2413373620","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26648810","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,"listed_in":[],"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":null,"is_accepted":false,"is_published":false,"raw_source_name":"PubMed","raw_type":null}],"best_oa_location":{"id":"pmh:oai:www.excli.de:article/1196","doi":null,"is_oa":true,"landing_page_url":"https://www.excli.de/excli/article/view/1196","pdf_url":"https://www.excli.de/excli/article/view/1196/2657","source":{"id":"https://openalex.org/S39273986","display_name":"EXCLI journal","issn_l":"1611-2156","issn":["1611-2156"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","ddh","doaj","dongbi-c","jufo-1","ki-jl-1","norway-1","oarl","poland-100","russia-white-list-1"],"host_organization":"https://openalex.org/P4310313779","host_organization_name":"IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund","host_organization_lineage":["https://openalex.org/P4310313779"],"host_organization_lineage_names":["IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"1611-2156","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1205728809.pdf","grobid_xml":"https://content.openalex.org/works/W1205728809.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1963723282","https://openalex.org/W1974889327","https://openalex.org/W1975447903","https://openalex.org/W1998848097","https://openalex.org/W2011956460","https://openalex.org/W2105668062","https://openalex.org/W2121895929","https://openalex.org/W2158534713","https://openalex.org/W2949243165","https://openalex.org/W3131944725"],"related_works":["https://openalex.org/W2413373620","https://openalex.org/W7096613652","https://openalex.org/W3133213603","https://openalex.org/W4402787892","https://openalex.org/W1984029386","https://openalex.org/W2336040088","https://openalex.org/W3086075983","https://openalex.org/W4321373401","https://openalex.org/W7214065004","https://openalex.org/W2730510844"],"abstract_inverted_index":{"Recently,":[0],"bioinformatics":[1,196],"has":[2,33],"advanced":[3],"to":[4,36,81,116,128,168,201],"the":[5,25,30,42,114,176],"level":[6],"that":[7,16,188],"it":[8],"allows":[9],"almost":[10],"accurate":[11],"prediction":[12],"of":[13,44,85,100,102,113],"molecular":[14,170,203],"interactions":[15],"hold":[17],"together":[18],"a":[19,22,38,83,98,110,120,189],"protein":[20],"and":[21,57,67,132,148,152,154,159,174],"ligand":[23],"in":[24,75,119,195,214],"bound":[26],"state.":[27],"For":[28],"instance,":[29],"program":[31,208],"AutoDock":[32,77,118,162,206],"been":[34],"developed":[35],"provide":[37],"procedure":[39],"for":[40,89,146],"predicting":[41],"interaction":[43],"small":[45],"molecules":[46,71],"with":[47,55,63,72,92,191],"macromolecular":[48],"targets":[49],"which":[50],"can":[51,68,78],"easily":[52],"separate":[53],"compounds":[54,91],"micromolar":[56],"nanomolar":[58],"binding":[59,65,94],"constants":[60,66],"from":[61,135],"those":[62],"millimolar":[64],"often":[69],"rank":[70],"finer":[73],"differences":[74],"affinity.":[76],"be":[79,199],"used":[80],"screen":[82],"variety":[84],"possible":[86],"compounds,":[87],"searching":[88],"new":[90],"specific":[93],"properties":[95],"or":[96],"testing":[97],"range":[99],"modifications":[101],"an":[103],"existing":[104],"compound.":[105],"The":[106,124,138,164],"present":[107],"work":[108],"is":[109,127,141,167,184],"detailed":[111],"outline":[112],"protocol":[115],"use":[117],"more":[121],"user-friendly":[122],"manner.":[123],"first":[125],"step":[126,140,166],"retrieve":[129],"required":[130],"Ligand":[131,149],"Target.pdb":[133],"files":[134,145],"major":[136],"databases.":[137],"second":[139],"preparing":[142],"PDBQT":[143],"format":[144],"Target":[147],"(Target.pdbqt,":[150],"Ligand.pdbqt)":[151],"Grid":[153],"Docking":[155],"Parameter":[156],"file":[157],"(a.gpf":[158],"a.dpf)":[160],"using":[161,172,205],"4.2.":[163],"third":[165],"perform":[169,202],"docking":[171,204],"Cygwin":[173],"finally":[175],"results":[177],"are":[178],"analyzed.":[179],"With":[180],"due":[181],"confidence,":[182],"this":[183,215],"our":[185],"humble":[186],"claim":[187],"researcher":[190],"no":[192],"previous":[193],"background":[194],"research":[197],"would":[198],"able":[200],"4.2":[207],"by":[209],"following":[210],"stepwise":[211],"guidelines":[212],"given":[213],"article.":[216]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":43},{"year":2024,"cited_by_count":49},{"year":2023,"cited_by_count":47},{"year":2022,"cited_by_count":51},{"year":2021,"cited_by_count":48},{"year":2020,"cited_by_count":54},{"year":2019,"cited_by_count":27},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":15},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2016-06-24T00:00:00"}
