Computational Biochemistry and Biophysics

Research Lines

Within the CBBL we use simulation techniques to understand the dynamical behavior of biological systems, at both molecular and systemic levels. The ultimate goal is to develop integrated multiscale modelsand to apply them to problems of biomedical relevance.

Biomolecular Function

In its origins, the group devoted its efforts to understand the effect of the different chemical groups in the protein-substrate interface and their influence in reactivity. The basic tools for this research are molecular dynamics simulations coupled to hybrid quantum mechanical/molecular mechanics approaches, in particular the simplified but extremely efficient EVB method developed by Warshel. Works on several biochemical systems during the postdoctoral stage at Warshel's lab have been followed by the work on the function of biomolecules, from enzymes to ion channels, how they move and fold and the way they interact.

Regulatory, protein and metabolic networks and their relationship with complex diseases

The trip the CBBL started in 2003 has lead to interesting bifurcations that are becoming main trunks in our research interests. One of the side products of the new interest in systems biology is represented by the exciting projects arising from the study of complex diseases at the biochemical level using not only systems biology techniques but also approaching the biomedical informatics paradigm. Thus, we are currently engaged in the study of diagnostic and eventually prognosis on rare diseases patients using an integrated knowledge management to clinical data through a simulation environment (see In addition, a new way of visualizing and accessing biological data through 3D virtual environments is being explored in the lab.

Development of HPC tools

The use of simulation techniques makes the CBBL an avid consumer of CPU time. Although the group is already involved in some projects regarding hard and soft infrastructure, the arrival of Gianni de Fabritiis, a Ramón y Cajal researcher, in the lab, has boosted our available technology to previously undreamed (for us) levels. Thus, the access to the PS3GRID and to the GPUGRID portals allows the CBBL to make extensive use of HPC resources that will help completing challenging simulations with the help of distributed and volunteer computing, in addition to the access to parallel supercomputing, depending on the specific task to perform.

This trip has lead us to see virtually no boundaries to what one can answer using simulation techniques. Clearly an opportunity for exciting new fields of research of the dynamical behavior of complex systems but also a warning for the need to find good descriptors of each and all types of individual interactions. A consensus between reductionist and complex views? maybe... keep tuned.

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