UDock

Udock v1

About UDock

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 Applications (GBA).

Download UDock

UDock is a free windows and linux standalone software. You can download an executable for windows here. The executable is inside the Bin directory and should not be moved. Alternatively, you can download the code source. here the windows version, and here the linux one

Usage

Udock accept mol2 file. You can either specify them as arguments when launching from the terminal, or add them while running by drag-n-dropping the mol2 file.

Docking

You can manipulate the molecules with the mouse. Place grapnels ont them by ctrl + left click. Delete them with ctrl + right click. You can adjust their positions with shift + left click.

Once satisfied with the grapnels positions, you can drag them together by pressing the "space" key.

The geometry of the complex can be automatically optimized at any time by pressing the "o" key. Note that you can select which will move by selecting it in the menu. Once the optimization is done, the molecules positions will be frozen for your convenience, you can unfreeze them by pressing the corresponding button on the menu.

You can save the current conformation of your complexes by pressing the save button, a corresponding PDB file will be created in the savefile directory.

Camera control

You can move the camera in a first person fashion by using the "w","a","s","d" key to change the position of the camera, and move the mouse while right-clicking to look around. You can also look around the focus (represented by a yellow sphere) by moving the mouse while shift + right-clicking. You can hide the focus 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.

Spaceship control

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.