Our team is one of the world-leading laboratories in classical molecular dynamics (MD) simulation studies on RNA molecules, including riboswitches and RNA catalysis. Besides investigations of specific biochemically important systems, we have been developing empirical potentials for MD simulations, i.e., force fields, that are used in many laboratories around the globe.
Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Ley AG, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M: RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem. Rev., 118(8), 4177–4338, 2018. (https://pubs.acs.org/doi/10.1021/acs.chemrev.7b00427)
Diarra dit Konté N, Krepl M, Damberger FF, Duss O, Šponer J, Allain FH: Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination. Nat. Commun., 8(654), 2017. (http://www.nature.com/articles/s41467-017-00631-3)
Havrila M, Stadlbauer P, Islam B, Otyepka M, Šponer J: Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes. J. Chem. Theory Comput., 13(8), 3911–3926, 2017. (https://pubs.acs.org/doi/10.1021/acs.jctc.7b00257)
Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P: Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. J. Chem. Theory Comput., 12(9), 4534–4548, 2016. (https://pubs.acs.org/doi/10.1021/acs.jctc.6b00300)
Šponer J, Banáš P, Jurečka P, Zgarbová M, Kührová P, Havrila M, Krepl M, Stadlbauer P, Otyepka M: Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. J. Phys. Chem. Lett., 5(10), 1771-1782, 2014. (https://pubs.acs.org/doi/10.1021/jz500557y)
FOR DETAILED DESCRIPTION OF RESEARCH AND COMPLETE LIST OF PUBLICATIONS SEE:
Research Group Leader
- RNA structural dynamics, folding and catalysis.
- Protein-RNA complexes.
- DNA, with focus on G-quadruplexes.
- Diverse types of quantum-chemical studies on nucleic acids systems.
- Origin of life (prebiotic chemistry), i.e., creation of the simplest chemical life on our planet (or anywhere else in the Universe).
- Understanding of the most basic principles of structural dynamics, function and evolution of DNA and RNA.
- Development of new methodologies for investigating the structure, interactions, and dynamics of biomolecules.
- Testing/parameterization of molecular mechanical force fields for DNA and RNA.
Content of research
We use a wide spectrum of state-of-the-art computational techniques, including explicit solvent molecular dynamics simulations, advanced ab initio quantum-chemical calculations and modern bioinformatics.