Research Lines
Mollecular Modeling
Structure-based design and discovery of protein ligands has emerged as a new tool in medicinal chemistry. In particular, the knowledge of the three-dimensional structure of a protein can be used to derive new protein ligands with improved binding properties ( i.e. new drugs ). Within this approach we need algorithms and methods to solve the following questions: What is the binding affinity of a novel ligand towards a particular receptor? What are the best conformations of a ligand to the binding site? What are the similarities of different ligands with respect to their recognition capabilities? With which orientation will a ligand bind to the active site? We want to contribute to obtain new answers for these questions and in particular for some problems concerning CANCER disease.
Molecular Dynamics
We apply molecular dynamics (MD) extensively using the AMBER and GROMACS suite of programs. MD is used to simulate the stability of protein dimers and of drug-protein complexes throughout time. We apply MD also to analyze the binding free energy of these complexes, employing the MMPBSA approximation.