Tutorials

User

Ligand-Protein Docking

Using AutoDock 4 with AutoDockTools

This tutorial teaches you how to use AutoDockTools to set up AutoGrid 4 grid map calculations, how to set up AutoDock 4 dockings, and how to analyse your docking results.

AutoDock Vina Video Tutorial

This video tutorial demonstrates molecular docking of imatinib using Vina with AutoDock Tools and PyMOL

Using AutoLigand with AutoDockTools

AutoLigand identifies and characterizes ligand binding sites in a macromolecule, using the grid-based energy evaluation method in AutoGrid.

Flexible rings docking

A step-by-step guide on how to dock flexible cyclic molecules with AutoDock 4.2

Using AutoDock 3.0.5 with AutoDockTools

This tutorial teaches you how to use AutoDockTools 3.0.5 to set up AutoGrid grid map calculations, how to set up AutoDock dockings, and how to analyse your docking results.

VI European Workshop on Drug Design - Molecular Docking Tutorial

This is a tutorial given in the VI European Workshop in Drug Design, in Certosa di Pontignano (Siena, Italy) and was prepared by Rino Ragno (RCMD), Anna Tramontano (BIOCOMPUTING), Adriano Marinelli (MMVSL) and Tiziano Tuccinardi (MMVSL). It describes how to use Chimera, AutoDockTools and AutoDock 4.0.1 to study Histone Deacetylase (HDAC) Inhibitors.

Virtual Screening

Using AutoDock 4 for Virtual Screening

This teaches you not only how to use AutoDock 4 to perform virtual screening using AutoDock 4, but also a lot about using UNIX to organize and process large numbers of files, skills that are transferable to many other problems. There is one PDF file (Handout) with step-by-step instructions, and another with the slides that accompany the presentation. The Handout includes instructions on how to download the necessary input files. When we teach this tutorial, we require that you have attended the "Using AutoDock 4 with AutoDockTools" tutorial.

Using AutoDock 3 for Virtual Screening

This teaches you not only how to use AutoDock 3 to perform virtual screening, but also a lot about using UNIX to organize and process large numbers of files, skills that are transferable to many other problems. There are two PDF files, the first contains slides describing some background to virtual screening and the overall process, and a second PDF file with step-by-step instructions. The latter includes instructions on how to download the necessary input files. When we teach this tutorial, we require that you have attended the "Using AutoDock with AutoDockTools" tutorial. NOTE: the tutorial currently refers to an incorrect CVSROOT location. The correct location should be: setenv CVSROOT :pserver:anonymous@moses.scripps.edu:/opt/cvs