In January 2008, I began working in the group of Modelling Chemical Reactivity (nonexistent nowadays) from the University of Oviedo under a ‘Clarín’ contract, a position funded by the Principado de Asturias government. In this new period I have been working in a line of research focused in the MD simulation of MMPs (Matrix Metalloproteinases) and triple helical peptides (THPs) as model systems of collagen, both in continuum and explicit solvent models. The model systems chosen contain non-standard residues, which necessarily required their previous specific parameterizations partially showing the complexity and dimension of the project. Part of this research has been already published in the Journal of the American Chemical Society (Valdés et al. J. Am. Chem. Soc. 130, 14070, 2008).
From October 2008 until September 2010, I have been working under the contract CTQ2007-63266 of the MICINN with the same above mentioned group on the same mentioned topic. The development of the project at that time required the use of docking techniques which I learnt to apply during my stay (2010) in the group Dr. Fernández-Recio at the Barcelona Supercomputing centre (BSC). As a result of this stay we have already published a paper in J. Chem. Theor. and Comput. 6, 2204, 2010 (first author).
During this period, I have also collaborated with the group of biorganic chemistry of the University of Oviedo and published a paper in the Chem. Eur. J. (Chem. Eur. J. 16, 11012, 2010) which has been selected for the cover of the corresponding issue.
The remaining research done during this period is yet to be finished since the MD simulations require huge amounts of computational resources and we are dependent on the time that we are assigned in the supercomputing centers along with the fact that these are not the unique projects carried out in the group and the computational hours available have to be shared by all its members. As the budget of the project was finished, I had to leave the group and join a different labotatory.