The Molecular Modeling and Bioinformatics (MMB) research group is part of the Joint BSC-CRG-IRB program in Computational Biology. This program between the Barcelona Supercomputing Center (BSC), the Institute for Research in Biomedicine (IRB-Barcelona) and the Center for Genomic Regulation (CRG) joins around 200 scientists working in the wide field of Computational Biology. Our long-term objective is to understand the behavior of living organisms from the basic rules of physics, in other words, to represent life by means of theoretical calculations.
Our efforts are currently focused in two major topics:
- The study of protein dynamics.
- The analysis of unusual or stressed DNAs of biological importance, with particular emphasis inchromatin-stressed DNAs.
Our group devotes a large effort in development of new methodologies, but also in the study of especially relevant biological systems. From the last five years our group has the experimental support from the IRB-BSC Experimental Bioinformatics Laboratory, where experimental validations are performed.
Our work in the period 2008-2013 is reflected in 96 scientific publications in peer-reviewed journals such asNature, Nature Genetics, Angew.Chem., Proc.Natl.Acad.Sci.USA., J.Am.Chem.Soc., Acc.Chem.Res., Nucleic Acids Res., Curr.Opin.Struct.Biol., Chem.Soc.Rev and many others. At the end of 2013 the group collected over 14000 citations.
We have contributed to the development of new SCRF methods based on the Polarizable Continuum Model of Pisa's group, extending its use to different solvents to the classical framework, and adapting them to the use in molecular modeling problems.
We have extended the GMIP(p) approach as a new effective Hamiltonian for QM/MM calculations of large systems and to use it as molecular property descriptor in drug-design projects.
We have developed a variety of tools for helping in drug-design projects. They include methods for the description of molecular properties, chemoinformatics and datamining tools, and advanced docking algorithms.
We are interested in the understanding of the basis of protein dynamics, how proteins transfer information and the coupling between dynamics and function.
Studies on anomalous Nucleic Acids
We are using molecular dynamics and statistical mechanics to study anomalous forms of nucleic acids. Particular attention is paid to the study of conformational transitions in DNA, drug-DNA interactions, and the analysis of unusual nucleic acid structures with potential use in antigene or antisense therapies.
Study of Chromatin
We are analyzing how physical properties of DNA modulates the structure and functionality of chromatin, trying to decipher an ancient physical code that helps in the control of gene function.
We are involved in the analysis of massive omics data, with special emphasis in: i) analysis and functional annotation of SNPS, ii) study of epigenetic variants and iii) analysis of chromatin structure.