Instituto Pasteur de Montevideo
Biomolecular Simulation Group
The Group of BioMolecular Simulations develops and applies cutting-edge modeling and simulation methods to the study of problems of biomedical relevance.
We develop and maintain a general-purposes Coarse-Grained (CG) force field for biomolecular systems, for which we coined the name SIRAH©. The force field currently includes parameters for simulating aqueous solvent and simple electrolytes; single/double stranded DNA and proteins at Coarse Grained and multiresolution level. A substantial effort has been devoted to make the implementation of SIRAH© user-friendly and straightforward in popular simulation packages. As a result, tarballs for using SIRAH© on Amber and Gromacs (the two most popular molecular dynamics simulation packages) along with step-by-step tutorials and scripts for analysis and visualization were made available from our web site (www.sirahff.com).
Instituto de Matemática Aplicada San Luis
January 2013
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December 2017
Bioinformatica Estructural (BIOS)
Our research group studies structural and dynamical properties of biomolecules and develops computational methods for the determination, validation and refinement of biomolecule structures, based on experimental data. The used tools include: quantum mechanical calculations, statistical mechanics, molecular dynamics and/or molecular mechanics simulations, and statistical data analysis.
