MOLECULAR BIOPHYSICS GROUP

COMPUTATIONAL BIOLOGY AREA

Group coordinator

Dr. Jesús Mendieta Gómez | j.mendieta.prof@ufv.es

Researchers
  • José María Bueno Calderón
External collaborating researchers

  • Jesús Ignacio Mendieta-Moreno

Research Summary

Application of Molecular Dynamics techniques to the study of the three-dimensional structure of biological macromolecules. Development and application of Quantum Mechanics/Molecular Mechanics (QM/MM) techniques to the study of enzymatic reactions. Rational design of drugs.

Line of research

  • Structural Biophysics and Mechanisms of Enzyme Action
Grado Biomedicina MOLECULAR BIOPHYSICS BIOTECHNOLOGY AREA Estudiar en Universidad Privada Madrid
Projects in the last 5 years
  • Ministry of Economy and Competitiveness. R+D+i projects research challenges project no. MAT2014-59966-R. 20152017 Title: Modeling of Materials at nanometric scale. PI: José Ortega Mateo
Publications
  • Proton Transfer in Guanine-Cytosine Base Pairs in B-DNA”. Soler-Polo D., Mendieta-Moreno J.I., Trabada D.G., Mendieta J. & Ortega J. (2019) J. Chem.Theory Comput. 15(12):6984-6991.
  • L Menedez-Arias; M Alvarez; M Nevot; J Mendieta; MA Martinez. (2018) “Amino acid residues in HIV-2 reverse transcriptase that restrict the development of nucleoside analogue resistance through the excision pathway”. Journal of Biological Chemistry. 293 – 7, pp. 2247-2259.
  • Dominguez, C.M.; Ramos, D.; Mendieta-Moreno, J.I.; Fierro, J.L.G.; Mendieta, J; Tamayo, J.; Calleja, M. (2017) “Effect of water-DNA interactions on elastic properties of DNA self- assembled monolayers.” Scientific Report. 7 – 1, pp. 536-544.
  • I Marcos-Alcalde; J Mendieta-Moreno; MC Gil-Rodriguez; M Hernandez-Marcos; D Soler-Polo; B Puisac; FJ Ramos; J Ortega; J Pie; J Mendieta; P Gomez-Puertas. (2017) “Two-step ATP driven opening of cohesin head” .Scientific Report. 7 – 1, pp. 3266-3273.
  • Jesus Ignacio Mendieta-Moreno; Daniel Trabada; Jesus Mendieta; James Lewis; Paulino Gomez-Puertas; Jose Ortega. (2016) “Quantum Mechanics / Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer.” Journal of Physical Chemistry Letters. 7, pp. 4391-4397.
  • J.I. Mendieta-Moreno; I. Marcos-aAlcalde; D.G. Trabada; P. Gomez-Puertas; J. Ortega; J. Mendieta. (2015) “A practical Quantum Mechanics Molecular Mechanics method for the dynamical study of reactions in biomolecules.” Advances in Protein Chemistry and Structural Biology. 100, pp. 67 – 88. 2015.
  • I. Marcos-Alcalde; J. Setoain; J.I. Mendieta-Moreno; J. Mendieta; P. Gomez-Puertas. (2015) “MEPSA: minimum energy pathway analysis for energy landscapes” . Bioinformatics. 31, pp. 3853-3855.
  • J.I. Mendieta-Moreno; R. Walker; J. Lewis; P. Gomez-Puertas; J. Mendieta; J. Ortega. (2014) “FIREBALL/AMBER: An efficient local-orbital DFT QM/MM method for biomolecular systems.” Journal of Chemical Theory and Computation. 10, pp. 2185 – 2193. 2014.
  • G. Betancor; M. Nevot; J. Mendieta; P. Gomez-Puertas; M.A. Martinez; L. Menendez-Arias. (2014) “Molecular basis of the association of H208Y and thymidine analogue resistance mutations M41L, L210W and T215Y in the HIV-1 reverse transcriptase of treated patients.” Antiviral Research. 106, pp. 42 – 52. 2014.
  • P. Gonzalez de Prado Salas; I. Hörger; F. Martín-García; J. Mendieta; A. Alonso; M. Encinar; P. Gómez-Puertas; M. Vélez; P. Tarazona. (2014) “Torsion and curvature of FtsZ filaments.” Soft Matter. 10, pp. 1977 – 1986.
j.mendieta.prof@ufv.es