Operating systems: MacOS and Linux.

Contacts : Nuno Sousa Cerqueira Pedro A. Fernandes Maria João Ramos

Citation :

VsLab—An implementation for virtual high-throughput screening using AutoDock and VMD.
N. M. F. S. A. Cerqueira, J. Ribeiro, P. A. Fernandes AND M. J. Ramos
International Journal of Quantum Chemistry, 2011, 111(6):1208–1212 DOI:10.1002/qua.22738

Molecular docking is becoming an important part in the process of developing new drugs. There is much docking software that has been successfully used in a myriad of keystone problems, however, as commonly happens with most of the scientific software, the programs are often complex and a deep knowledge is required for the common user to carry out standard steps.

This is an obstacle and a cornerstone issue for the research teams in the fields of Chemistry and the Life Sciences, who are interested in conducting this kind of calculations but do not have enough programming skills.

To overcome these limitations, we have designed vsLab (Virtual Screening LABoratory), an easy-to-use graphical interface for the well known molecular docking software AutoGrid/AutoDock that has been included into VMD as a plug-in. This program allows almost anyone to use AutoDock and AutoGrid for simple docking or for virtual screening campaigns without requiring any deep knowledge about these techniques.

The potential associated to this software makes it an attractive choice not only for educational purposes, but also for more advanced users that can use vsLab to increase workflow and productivity of everyday tasks.

In order to run the vsÇab plug-in, the Visual Molecular dynamics software (VMD) must be installed. It can be found at http://www.ks.uiuc.edu/Research/vmd/ .

VsLab can only be installed in LINUX and MAC operating systems, due to the limitations of the autodock software. Installation in Windows will be available whenever possible.

Two programs must be installed in order to run vsLab:

1. The program VMD (http://www.ks.uiuc.edu/Research/vmd )
2. The sqlite database engine (http://www.sqlite.org)
3. AutoDock Suite (http://autodock.scripps.edu)

The first program can be easily installed with the tutorials available in the VMD site ( version 1.8.7 is required).

The sqlite database engine is generally installed in all UNIX/LINUX systems (to see if it is installed just write in the terminal: sqlite) If it is not installed you can install writing the following commands in the terminal under the root privileges:

 Ubuntu OS : sudo apt-get install sqlite
 fedora OS : yum install sqlite
 Mac       : (see user manual)

VsLab also depends on autodock and autogrid executables. Therefore they must be installed in the systems before the installation of vLab proceeds.

The installation of AutoDockTools program is also required.

Only three steps are required to run VsLab:

• Unordered List ItemExtract the file vsLab.tar.gz to a directory of your choice.

 tar -xvzf vsLab.tar.gz

• Run the program install.tcl and follow the instructions:

 cd vsLab
 tclsh install.tcl

Then the user just have to follow the guidelines that are provided by the script.

After the installation ends you can find vsLab inside VMD application, at the plug-in the menu: Extensions» PortoBioComp»virtal screening Lab

not available yet.

7.1. Ligand Preparation

The name of the ligands should not have symbols. For instance the name compound-1.mol2 should be avoided, and the name compound1.mol2 should be used instead.