Guide to Docking with AutoDock ----------------------------- > Working with PPARs? Then it is essential for you to learn about > molecular docking. Working with AB or IAPP? You most likely will not > utilize molecular docking; however, if you would like to learn more > about it, here is your chance! You will need to use AutoDock Tools and > AutoDock vina, both found on a lab computer by using terminal to > execute the command for the program. (adt for AutoDock Tools and vina > for Autodock Vina). ADT and vina can also be installed on your > personal computer (Mac or PC). To download AutoDock tools go > [here][1], and to download Autodock Vina go [here][2]. ## AutoDock 4.0 and AutoDockTools 1.5.2 Tutorial ## > This tutorial is meant to be a condensed version of information available online through the developer sites for in-lab purposes. Portions of the AutoDock and ADT information were taken verbatim from the tutorials written by Ruth Huey and Garrett M. Morris (References on final page). If anything is unclear or more detailed information is desired, please consult the original tutorials. [Read More][3] ## Re-Docking and Cross-Docking ## *The re-docking tutorial is written under the assumption that you have done the docking tutorial in step A.* > For the purposes of this tutorial, you will use crystal structures to perform re-docking and cross- docking. Re-docking refers to the ability to reproduce co-crystallized binding geometry and orientation of the associated ligand given a rigid macromolecule state. Cross-docking refers to utilizing different ligand structures isolated from multiple PDB files of the same protein to test against a single rigid protein model structure. In both cases, success is relative to root mean- squared deviation (RMSD) between the docked pose and the respective crystal conformer. RMSD values less than 2.0 Å are considered good, but values closest to zero are ideal. [Read More][4] [1]: http://mgltools.scripps.edu/downloads [2]: http://vina.scripps.edu/download.html [3]: https://drive.google.com/file/d/113po1HdJ8XbLsu5dfgk1HUMLMZDNy7_X/view?usp=sharing [4]: https://drive.google.com/file/d/1KsqByHYcdGJ-H12w9Gr9gW2ktZD86wdb/view?usp=sharing [5]: https://drive.google.com/open?id=0B3HZsuBIsg47Ym42RDVwRlVWWHM