Volarea - A Bioinformatics Tool to Calculate the Surface Area and the Volume of Molecular Systems

• Type: Article in International Scientific Journal
• Date: 2013

Authors

Joao V Ribeiro (Author) Other; Juan A C Tamames (Author) Other; Nuno M F S A Cerqueira (Author) FCUP; Pedro A Fernandes (Author) FCUP; Maria J Ramos (Author) FCUP

Journal

Title: Chemical Biology and Drug Design

Vol. 82

Pages: 743-755

ISSN: 1747-0277

Publisher: Wiley-Blackwell

Indexing

ISI Web of Knowledge - 25 Citations

Scopus - 26 Citations

Scientific classification

FOS: Medical and Health sciences > Basic medicine

Other information

Authenticus ID: P-008-JDC

DOI: 10.1111/cbdd.12197

Abstract (EN): We have developed a computer program named VolArea' that allows for a rapid and fully automated analysis of molecular structures. The software calculates the surface area and the volume of molecular structures, as well as the volume of molecular cavities. The surface area facility can be used to calculate the solvent-exposed surface area of a molecule or the contact area between two molecules. The volume algorithm can be used to predict not only the space occupied by any molecular structure, but also the volume of cavities, such as tunnels or clefts. The software finds wide application in the characterization of systems, such as protein/ligand complexes, enzyme active sites, protein/protein interfaces, enzyme channels, membrane pores, solvent tunnels, among others. Some examples are given to illustrate its potential. VolArea is as a plug-in of the widely distributed software Visual Molecular Dynamics (VMD) and is freely available at http://www.fc.up.pt/PortoBioComp/Software/Volarea/Home.html.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 13