Sunday, 25th June 2017

Virology and Microbiology

    Molecular modelling group



 GMM atom


Paulino Gómez-Puertas




Please find more detailed information about the group and our research here:

Researchers:Paulino Gómez-Puertas (PI), Jesús Mendieta Gómez, Jesús I. Mendieta Moreno, Íñigo Marcos Alcalde, Silvia Lusa Bernal.

Research Summary:

Integration of evolutive and structural information to study the function of proteins. Simulation of dynamic processes of protein-protein and protein-ligand interaction. Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approaches. Development of novel "in silico" drug design systems. Next-Generation Sequencing (NGS) Data Analysis.

Current projects:

Development of a more efficient and accurate system of QM/MM approach (FIREBALL/AMBER) for the computer simulation of enzymatic reactions. The use of Quantum Mechanics / Molecular Mechanics (QM/MM) interfaces allow the simultaneous use of both approaches in the study of complex reactions such as those occurring at the active centre of molecules of biological interest (biomolecules). From the 70s to the present, QM/MM simulation methods had to choose between accuracy (using computationally expensive ab-initio systems for the QM part) and computational efficiency (using semiempirical Hamiltonians that allow for a much faster calculation). In collaboration with the group of Dr. José Ortega Mateo (Department of Theoretical Condensed Matter Physics, UAM), we have developed a new QM/MM simulation method, called FIREBALL/AMBER, with a theory level similar to Gaussian but several hundred times more efficient, which represents a major step forward for the computer simulation of bioprocesses. The project involves both the development and refinement of the system and its application to the study of enzymatic reactions in proteins of interest to biomedicine: Cohesins SMC1A-SMC3, HIV-RT, FoF1-ATPase, Carnitine acyltransferases, the bacterial protein FtsZ, etc.

Molecular dynamics simulation of polymerization and depolymerization processes of bacterial septum protein FtsZ. Design of specific inhibitors to be used as antibacterial drugs using "in silico" drug design systems based on the properties of the receptor molecule. This project is developed in the framework of an R&D contract between Biomol-Informatics and the Fundación "Severo Ochoa".


More information:

Most relevant publications, last years (see full list here):

  • Marcos-Alcalde, I., Mendieta-Moreno, J.I., Puisac, B., Gil-Rodríguez, M.C., Hernández-Marcos, M., Soler-Polo, D., Ramos, F.J., Ortega, J., Pié, J., Mendieta, J. & Gómez-Puertas, P. (2017). Two-step ATP-driven opening of cohesin head. Scientific Reports 7, 3266.
  • Marcos-Alcalde, I., Setoain, J., Mendieta-Moreno, J.I., Mendieta, J. & Gómez-Puertas, P. (2015). MEPSA: minimum energy pathway analysis for energy landscapes. Bioinformatics 31, 3853-3855.

  • Mendieta-Moreno, J., Walker, R., Lewis, J., *Gómez-Puertas, P., Mendieta, J. & *Ortega, J. (*Corresponding authors) (2014). FIREBALL/AMBER: An efficient local-orbital DFT QM/MM method for biomolecular systems. Journal of Chemical Theory and Computation 10, 2185–2193.

  • Martín-García, F., Mendieta-Moreno, J.I., Marcos-Alcalde, I, *Gómez-Puertas, P. & Mendieta, J. (*Corresponding author). (2013). Simulation of catalytic water activation in mitochondrial F1-ATPase using a hybrid quantum mechanics/molecular mechanics approach: An alternative role for ß-Glu 188. Biochemistry 52, 959-966.