Using the maximum entropy principle to combine simulations and solution experiments
Molecular dynamics (MD) simulations allow the investigation of the structural dynamics of
biomolecular systems with unrivaled time and space resolution. However, in order to …
biomolecular systems with unrivaled time and space resolution. However, in order to …
Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions
Abstract The International Society of RNA Nanotechnology and Nanomedicine (ISRNN)
serves to further the development of a wide variety of functional nucleic acids and other …
serves to further the development of a wide variety of functional nucleic acids and other …
Improving the performance of the amber RNA force field by tuning the hydrogen-bonding interactions
Molecular dynamics (MD) simulations became a leading tool for investigation of structural
dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force …
dynamics of nucleic acids. Despite recent efforts to improve the empirical potentials (force …
Interrogating RNA–small molecule interactions with structure probing and artificial intelligence-augmented molecular simulations
While there is increasing interest in the study of RNA as a therapeutic target, efforts to
understand RNA-ligand recognition at the molecular level lag far behind our understanding …
understand RNA-ligand recognition at the molecular level lag far behind our understanding …
Toward convergence in folding simulations of RNA tetraloops: Comparison of enhanced sampling techniques and effects of force field modifications
Atomistic molecular dynamics simulations represent an established technique for
investigation of RNA structural dynamics. Despite continuous development, contemporary …
investigation of RNA structural dynamics. Despite continuous development, contemporary …
Automatic learning of hydrogen-bond fixes in the AMBER RNA force field
T Frohlking, V Mlýnský, M Janeček… - Journal of Chemical …, 2022 - ACS Publications
The capability of current force fields to reproduce RNA structural dynamics is limited. Several
methods have been developed to take advantage of experimental data in order to enforce …
methods have been developed to take advantage of experimental data in order to enforce …
Fitting corrections to an RNA force field using experimental data
A Cesari, S Bottaro, K Lindorff-Larsen… - Journal of chemical …, 2019 - ACS Publications
Empirical force fields for biomolecular systems are usually derived from quantum chemistry
calculations and validated against experimental data. We here show how it is possible to …
calculations and validated against experimental data. We here show how it is possible to …
Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA
structure. A number of forward models that relate measured SAXS intensities and structural …
structure. A number of forward models that relate measured SAXS intensities and structural …
Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes
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 …
thanks to the increasing amount of structural data exploitable for the rational design of …
Accelerating the ensemble convergence of RNA hairpin simulations with a replica exchange structure reservoir
K Lam, K Kasavajhala, S Gunasekera… - Journal of chemical …, 2022 - ACS Publications
RNA is a key participant in many biological processes, but studies of RNA using computer
simulations lag behind those of proteins, largely due to less-developed force fields and the …
simulations lag behind those of proteins, largely due to less-developed force fields and the …