Strategic Research

Protein Interactions and Docking

Our research focuses on the study of biomolecular interactions, which control the majority of biological processes in a highly specialized manner. We develop and apply computational approaches to characterize and understand protein interactions at molecular level.  with practical applications to biomedical problems.  For that, we are working on algorithmic solutions, based on physico-chemical principles, with the help of high-performance computing (HPC) resources. On the most practical side, we want to provide rationale for protein interactions of biological and therapeutic interest, and contribute to drug discovery targeting protein-protein interactions.

Main projects

  • 1.

    Structural modeling of protein interactions

    We are developing computational methods for the structural modeling of protein interactions. Our aim is to solve current challenges in the field, such as the treatment of conformational flexibility in docking, prediction of weak-affinity complexes, integration of low-resolution structural data from SAXS or EM, study of protein-DNA and protein-RNA interactions, or multi-scale modeling of macro-complexes. These tools are being optimized for their implementation in HPC, which will facilitate their application at interactomic scale.

  • 2.

    Study of protein interactions of biomedical interest

    In collaboration with experimental laboratories, we use our computational models for the structural characterization of specific complexes of biological and biomedical interest. One of the important challenges is to contribute to drug design targeting protein-protein interactions by means of binding site prediction, analysis of ‘hot-spots’ and identification of transient interface cavities.

  • 3.

    Characterization of pathological variants involved in protein interactions

    We are mapping pathological mutations on structural models of protein interactions at large scale, in order to understand better the effect of sequence variants in the development of disease and/or drug response. Our protein interaction predictions can help to interpret data from available databases and on-going genomics projects and complement current efforts towards personalized medicine.