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

• Tipo: Artigo em Revista Científica Internacional
• Data: 2013

Autores

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

Revista

Título: Chemical Biology and Drug Design

Vol. 82

Páginas: 743-755

ISSN: 1747-0277

Editora: Wiley-Blackwell

Indexação

ISI Web of Knowledge - 25 Citações

Scopus - 26 Citações

Classificação Científica

FOS: Ciências médicas e da saúde > Medicina básica

Outras Informações

ID Authenticus: 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.

Idioma: Inglês

Tipo (Avaliação Docente): Científica

Nº de páginas: 13