Investigating RNA–protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations
Ribonucleic acid (RNA) plays a key regulatory role within the cell, cooperating with proteins
to control the genome expression and several biological processes. Due to its characteristic …
to control the genome expression and several biological processes. Due to its characteristic …
How 'protein-docking'translates into the new emerging field of docking small molecules to nucleic acids?
F Tessaro, L Scapozza - Molecules, 2020 - mdpi.com
In this review, we retraced the '40-year evolution'of molecular docking algorithms. Over the
course of the years, their development allowed to progress from the so-called 'rigid …
course of the years, their development allowed to progress from the so-called 'rigid …
Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8–17 DNAzyme in solution
We perform molecular dynamics simulations, based on recent crystallographic data, on the 8–
17 DNAzyme at four states along the reaction pathway to determine the dynamical …
17 DNAzyme at four states along the reaction pathway to determine the dynamical …
DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL
XJ Lu - Nucleic acids research, 2020 - academic.oup.com
Sophisticated analysis and simplified visualization are crucial for understanding complicated
structures of biomacromolecules. DSSR (Dissecting the Spatial Structure of RNA) is an …
structures of biomacromolecules. DSSR (Dissecting the Spatial Structure of RNA) is an …
The architecture of the 10‐23 DNA zyme and its implications for DNA‐mediated catalysis
J Borggräfe, CGW Gertzen, A Viegas… - The FEBS …, 2023 - Wiley Online Library
Understanding the molecular features of catalytically active DNA sequences, so‐called
DNAzymes, is essential not only for our understanding of the fundamental properties of …
DNAzymes, is essential not only for our understanding of the fundamental properties of …
RNA electrostatics: how ribozymes engineer active sites to enable catalysis
Electrostatic interactions are fundamental to RNA structure and function, and intimately
influenced by solvation and the ion atmosphere. RNA enzymes, or ribozymes, are catalytic …
influenced by solvation and the ion atmosphere. RNA enzymes, or ribozymes, are catalytic …
[HTML][HTML] Targeting non-coding RNAs: Perspectives and challenges of in-silico approaches
The growing information currently available on the central role of non-coding RNAs
(ncRNAs) including microRNAs (miRNAS) and long non-coding RNAs (lncRNAs) for chronic …
(ncRNAs) including microRNAs (miRNAS) and long non-coding RNAs (lncRNAs) for chronic …
Hydration free energies and solvation structures with molecular density functional theory in the hypernetted chain approximation
S Luukkonen, M Levesque, L Belloni… - The Journal of Chemical …, 2020 - pubs.aip.org
The capability of molecular density functional theory in its lowest, second-order
approximation, equivalent to the hypernetted chain approximation in integral equations, to …
approximation, equivalent to the hypernetted chain approximation in integral equations, to …
Dynamics of Cations around DNA and Protein as Revealed by 23Na Diffusion NMR Spectroscopy
Counterions are vital for the structure and function of biomolecules. However, the behavior
of counterions remains elusive due to the difficulty in characterizing mobile ions. Here, we …
of counterions remains elusive due to the difficulty in characterizing mobile ions. Here, we …
Semi-empirical and linear-scaling DFT methods to characterize duplex DNA and G-quadruplexes in the presence of interacting small molecules
IO de Luzuriaga, S Elleuchi, K Jarraya… - Physical Chemistry …, 2022 - pubs.rsc.org
The computational study of DNA and its interaction with ligands is a highly relevant area of
research, with significant consequences for developing new therapeutic strategies …
research, with significant consequences for developing new therapeutic strategies …