Research Fields
Enzymology is one of the fields to which we are more devoted. We study the catalytic mechanism of enzymes using computational methods such as DFT and DLPNO-CCSD(T) combined with molecular mechanics through QM/MM methodologies. In addition, we develop methods for rational enzyme evolution.
The molecular dynamics of proteins is also an important field of research. We conduct free energy calculations of several processes, such as protein-ligand binding, conformational rearrangements, or passive diffusion of small druglike molecules along cell membranes and membrane-inserted porins.
We also work in alanine scanning mutagenesis (ASM). We develop new methodologies to carry out computationally this demanding experimental technique. For so, we mutate every single residue of a protein-protein interface by alanine and calculate the mutation impact on the binding free energy of two proteins. This powerful method is state-of-the-art for the experimental analysis of protein binding interfaces.
Our computational method is as accurate as the most demanding computational alchemical methods, even though it costs just a tiny fraction of the computational time.
We work in protein-protein docking. We have been developing scoring functions that can discriminate native structures among decoy structures with a very high confidence level. The success in picking a native structure in the top-ranked position is around 90%.
We have been developing software for the last few years. MADAMM, VSLab, CompASM are the ones that have already been made available to the scientific community. MADAMM performs flexible docking within a multi-scale philosophy.
VSLab offers a convenient and straightforward way of conducting virtual screening campaigns with AutoDock, simplifying all computational procedures and offering additional analysis tools. CompASM is a tool that performs and analyses Alanine Scanning Mutagenesis of proteins interfaces (using the Amber software) in a simple, convenient, and semi-automated way. All these algorithms are directed to facilitate drug discovery, which we carry out with the collaboration of fellow experimentalists and industrial partners.
The subjects we are most interested in are snake venom and plastic-degrading enzymes.
We study the reaction mechanism and pathophysiology of enzymes and proteins of snake venoms. Besides the fundamental interest in understanding one of the most complex bioactive cocktails Nature has ever created, we develop new antidotes for treating snakebite. In addition, we are creating new venom-inspired drugs.
Concerning the bio-recycling of plastics, we study enzymes that degrade several environmentally challenging plastics. PET (the plastic used to make bottles) is one example. We further engineer the enzymes to make them more efficient for industrial-scale recycling.