Udock is a free interactive protein docking system, intended for both naive and experienced users. UDock is developed at the Conservatoire National des Arts et Metiers, France, by the Centre d'Etudes et de Recherche en Informatique et Communications (CEDRIC) and the Laboratoire de Genomique, Bioinformatique, et Chimie Moleculaire (GBCM).
UDock is a free windows and linux standalone software. You can download an executable for windows here. You can download an executable for linux here. The executable is inside the Release directory and should not be moved.
Udock accepts mol2 files. You can either specify them as arguments from the terminal (./UDock2_Win.exe file.mol2 file2.mol2..), or drag-n-drop the mol2 files from your filesystem.
You can manipulate the molecules using the mouse. Place grapnels on the molecules using ctrl + left click. Delete the grapnels using ctrl + right click. You can adjust the grapnels with shift + left click. You can add as many grapnels as you like.
Once satisfied with the position of the grapnels, you can start the docking by pulling the grapnels holding the "space bar".
The geometry of the complex can be automatically optimized at any time by pressing the "o" key. Note that you can select the molecule for which the geometry will be optimized by selecting its corresponding "radio" button in the menu. Once the optimization is done, the molecules positions will be frozen for your convenience, you can unfreeze them by pressing "unfreeze" on the menu.
You can export the geometry of your protein-protein complexes by pressing the save button, the corresponding mol2 files will be created in the savefile directory.
You can use the freefly camera by using the "w","a","s","d" keys to change the position of the camera, and move the mouse while right-clicking to look around. You can also look around the focus point (represented by a large yellow sphere) by holding the shift+right-click keys. You can display and hide the focus point by pressing the "f" key.
Note that you can change the mouse sensitivity and inverse the y-axis inside the option menu.
Alternatively, if you have a xbox gamepad connected, you can move the camera laterally with the left stick and rotate it with the right stick. You can move forward by pressing the right trigger and backward by pressing the left one.
By pressing the "tab" key, you can switch to the spaceship mode. You can move the spaceship by using the "w","a","s","d" key. you can roll around the forward axis with the "q" and "e" key. You can direct the view with the mouse and interact with the molecule by left clicking. You can change the mode of interaction with the "r" key.
The three mode of interaction are : modifying the position of a grapnel, pulling the molecule toward the spaceship, pushing the molecule.
You can switch between the interior and exterior view with the "v" key.
Alternatively, if you have a xbox gamepad connected, you can move the camera laterally with the left stick and rotate it with the right stick. You can move forward by pressing the right trigger and backward by pressing the left one. You can roll around the forward axis with the shoulder button. You can activate the interaction mode by pressing the "A" button and select the interaction mode with the horizontal button on the D-pad. You can change between view with the "Y" button. Finally you can reset the scene by pressing the back button.