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Mg2+ ions: do they bind to nucleobase nitrogens?
A potential Zn2+ ribosomal binding site involving two purine N7 atoms is described and a set of guidelines are provided to help in the assignment of Mg2+ in crystallographic, cryo-EM, NMR and model building practices. Expand
‘Z-DNA like’ fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response
- Luigi D’Ascenzo, F. Leonarski, Q. Vicens, P. Auffinger
- Biology, Medicine
- Nucleic acids research
- 5 May 2016
Over 600 instances of Z-like steps are reported, which are located within r(UNCG) tetraloops but also in small and large RNAs including riboswitches, ribozymes and ribosomes, which could be a key to understanding the immune response at a structural level. Expand
The JUNGFRAU Detector for Applications at Synchrotron Light Sources and XFELs
Binding of metals to purine N7 nitrogen atoms and implications for nucleic acids: A CSD survey
Abstract Understanding the structure and function of RNA and DNA systems depends partly on our comprehension of the binding features of metal ions to nucleobases. Such knowledge is important for an… Expand
New more accurate calculations of the ground state potential energy surface of H(3) (+).
- M. Pavanello, W. Tung, F. Leonarski, L. Adamowicz
- Chemistry, Medicine
- The Journal of chemical physics
- 18 February 2009
Explicitly correlated Gaussian functions with floating centers have been employed to recalculate the ground state potential energy surface (PES) of the H(3) (+) ion with much higher accuracy than it… Expand
Revisiting GNRA and UNCG folds: U-turns versus Z-turns in RNA hairpin loops.
It is shown that some structured tetranucleotide sequences starting with G or U can adopt either of these folds, and a general view on the inclination for a given sequence to adopt (or not) a specific fold is proposed. Expand
Non-adiabatic corrections to the energies of the pure vibrational states of H2
Abstract Nonrelativistic energies of all fifteen pure vibrational states of the H 2 molecule have been recalculated with much higher accuracy than before. In the calculations we employed explicitly… Expand
Nucleobase carbonyl groups are poor Mg2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey.
Evidence derived from X-ray structures that nucleobases are poor inner-sphere binder for Mg2+ but good binders for monovalent ions is provided and an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms are proposed. Expand
Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field.
- F. Leonarski, Fabio Trovato, V. Tozzini, A. Les, J. Trylska
- Computer Science, Medicine
- Journal of chemical theory and computation
- 21 October 2013
This work presents an automatic method that implements an evolutionary algorithm to find a set of optimal force field parameters for a one-bead coarse-grained model and applies it to the dynamics of an RNA helix and the RNA structure prediction. Expand
Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector
The application of a direct-detection charge-integrating pixel-array detector (JUNGFRAU) in macromolecular crystallography (MX) that features a uniform response on the subpixel level, linear behavior toward high photon rates, and low-noise performance across the whole dynamic range is described. Expand