Computer simulations and computer modeling are fundamental tools for the
understanding the relationships between structure and function of
In our group, we aim to develop new computational tools and simulation
strategies to study the structure and dynamics of biological
macromolecules in solution. We stimulate students to develop computer programming skills
in order to develop novel modeling or data-analysis methods.
Computational tools developed in our group include the widely used
Packmol package for building initial configurations for
molecular dynamics simulations, and the TopoLink program
for the analysis of chemical-crosslinking distance constraints. Fast and
versatile packages for structural alignment and analysis of MD
simulations are also available as free software.
Currently, we focus in two major research topics: 1) Modeling the
tertiary structure of proteins using distance constraints, particularly
those derived from chemical-crosslinking mass-spectrometry, and 2) the
understanding of the solvation structure of solutes of complex
structure. On-demand application of molecular modeling and simulations
to the understanding of specific bimolecular systems is also recurrent.
We have tight interaction with
experimental groups, and we hope to suggest from the computational
models new hypothesis that should be testable by experiments.
The group is also experienced in the application of large-scale
optimization techniques to problems arising in computational chemistry