Giovanni Pinamonti

TL;DR: An in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods are covered.

TL;DR: Barnaba is a Python library aimed at facilitating the analysis of nucleic acid structures and molecular simulations, and produces graphics that conveniently visualize both extended secondary structure and dynamics for a set of molecular conformations.

TL;DR: In this article, various families of elastic networks of increasing complexity applied to a representative set of RNAs are evaluated by comparison against extensive molecular dynamics simulations and SHAPE experiments. And they find that simulations and experimental data are systematically best reproduced by either an all-atom or a three-beads-per-nucleotide representation (sugar-base-phosphate), with the latter arguably providing the best balance of accuracy and computational complexity.

TL;DR: This work considers various families of elastic networks of increasing complexity applied to a representative set of RNAs and finds that simulations and experimental data are systematically best reproduced by either an all-atom or a three-beads-per-nucleotide representation, with the latter arguably providing the best balance of accuracy and computational complexity.

TL;DR: It is shown that when the correct coarsening resolution is used not only do the optimized models match the Reference model simulated experimental data accurately but additional observables not directly targeted during the optimization procedure are also reproduced.