Operating systems: Windows, MacOS and Linux.

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

Citation :

A VMD Plug-in to measure the Surface and calculate the Volume of proteins.
J. Ribeiro, N. M. F. S. A. Cerqueira, , P. A. Fernandes AND M. J. Ramos
Chemical Biology & Drug Design, 2013, in press

VolArea is a plug-in of the widely spread molecular graphics software Visual Molecular Dynamics (VMD), which allows the calculation of the volume as well as the surface area of any chemical structure.

The surface area can be used also to map or calculate the exposed area of the structure to the solvent or to another chemical structure. This is particularly useful to characterize protein:ligand complexes or corresponding binding sites, as well as protein:protein interfaces. The volume algorithm can be used to predict the space occupied by any chemical structure as well as that of cavities, such as tunnels, clefts, etc.

Running VolArea only requires a few instructions from the user that are managed by a very intuitive graphical interface. The results of the calculations are presented in two different sections: one is devoted to the surface area of the structure under study and the other to its volume. These values can be analyzed in three different ways: 1. using the VMD graphical interface window 2. in an xy plot and 3. in other softwares by exporting the data in txt format.

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

The compASM plug-in runs in any platform where VMD runs, i.e., Windows, OSX and LINUX.

1. Install the VMD software ( if you haven't yet installed).
2. Extract vmdMagazine.zip file to a directory in the disk.
3. Once unpacked, we need to let VMD know of this location. To do so, edit your VMD start-up file and add the biopathfinder plugin directory to the auto_path variable (see below).
4. Once this procedure is complete the BioPathFinder plugin can be found at the VMD extensions menu (CompBioComp»vmdMagazine).