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dc.creatorValdés-Tresanco M.S.
dc.creatorValdés-Tresanco M.E.
dc.creatorValiente P.A.
dc.creatorMoreno E.
dc.date2020
dc.date.accessioned2021-02-05T14:57:53Z
dc.date.available2021-02-05T14:57:53Z
dc.identifier.issn17456150
dc.identifier.urihttp://hdl.handle.net/11407/5916
dc.descriptionAMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock Vina and AutoDock4, including the option of using the Autodock4Zn force field for metalloproteins. AMDock integrates several external programs (Open Babel, PDB2PQR, AutoLigand, ADT scripts) to accurately prepare the input structure files and to optimally define the search space, offering several alternatives and different degrees of user supervision. For visualization of molecular structures, AMDock uses PyMOL, starting it automatically with several predefined visualization schemes to aid in setting up the box defining the search space and to visualize and analyze the docking results. One particularly useful feature implemented in AMDock is the off-target docking procedure that allows to conduct ligand selectivity studies easily. In summary, AMDock's functional versatility makes it a very useful tool to conduct different docking studies, especially for beginners. The program is available, either for Windows or Linux, at https://github.com/Valdes-Tresanco-MS . REVIEWERS: This article was reviewed by Alexander Krah and Thomas Gaillard.
dc.language.isoeng
dc.publisherNLM (Medline)
dc.relation.isversionofhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85091128116&doi=10.1186%2fs13062-020-00267-2&partnerID=40&md5=15c05e9ec1884e63306a5e744ef22dba
dc.sourceBiology direct
dc.subjectAMDockspa
dc.subjectAutoDock Vinaspa
dc.subjectAutoDock4spa
dc.subjectAutoDock4Znspa
dc.subjectDockingspa
dc.subjectGraphical user interfacespa
dc.titleAMDock: a versatile graphical tool for assisting molecular docking with Autodock Vina and Autodock4
dc.typeArticleeng
dc.rights.accessrightsinfo:eu-repo/semantics/restrictedAccess
dc.identifier.doi10.1186/s13062-020-00267-2
dc.relation.citationvolume15
dc.relation.citationissue1
dc.relation.citationstartpage12
dc.publisher.facultyFacultad de Ciencias Básicasspa
dc.affiliationValdés-Tresanco, M.S., Faculty of Basic Sciences, University of Medellin, Medellin, Colombia
dc.affiliationValdés-Tresanco, M.E., Center of Protein Studies, Faculty of Biology, University of Havana, La Habana, 10400, Cuba, Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
dc.affiliationValiente, P.A., Center of Protein Studies, Faculty of Biology, University of Havana, La Habana, 10400, Cuba, Present address: Donnelly Centre for Cellular & Biomolecular Research University of Toronto, ON, 160 College St, Toronto, M5S 3E1, Canada
dc.affiliationMoreno, E., Faculty of Basic Sciences, University of Medellin, Medellin, Colombia
dc.type.versioninfo:eu-repo/semantics/publishedVersion
dc.type.driverinfo:eu-repo/semantics/article


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