Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes.

ABSTRACT: Ribonucleic acids are gradually becoming relevant players among putative drug targets, thanks to the increasing amount of structural data exploitable for the rational design of selective and potent binders that can modulate their activity. Mainly, this information allows employing different computational techniques for predicting how well would a ribonucleic-targeting agent fit within the active site of its target macromolecule. Due to some intrinsic peculiarities of complexes involving nucleic acids, such as structural plasticity, surface charge distribution, and solvent-mediated interactions, the application of routinely adopted methodologies like molecular docking is challenged by scoring inaccuracies, while more physically rigorous methods such as molecular dynamics require long simula

SUBMITTER: Dodaro A 

PROVIDER: S-EPMC10679717 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature