New developments in force fields for biomolecular simulations
Highlights•Biomolecular force fields (FFs) have progressed rapidly in the past five
years.•Fixed-charge FF accuracy has improved, but challenges remain for complex …
years.•Fixed-charge FF accuracy has improved, but challenges remain for complex …
The dynamic, motile and deformative properties of RNA nanoparticles facilitate the third milestone of drug development
Besides mRNA, rRNA, and tRNA, cells contain many other noncoding RNA that display
critical roles in the regulation of cellular functions. Human genome sequencing revealed that …
critical roles in the regulation of cellular functions. Human genome sequencing revealed that …
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 …
Simple adjustment of intranucleotide base-phosphate interaction in the ol3 amber force field improves RNA simulations
Molecular dynamics (MD) simulations represent an established tool to study RNA
molecules. The outcome of MD studies depends, however, on the quality of the force field …
molecules. The outcome of MD studies depends, however, on the quality of the force field …
Software Infrastructure for Next-Generation QM/MM− ΔMLP Force Fields
We present software infrastructure for the design and testing of new quantum
mechanical/molecular mechanical and machine-learning potential (QM/MM− ΔMLP) force …
mechanical/molecular mechanical and machine-learning potential (QM/MM− ΔMLP) force …
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 …
On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules
RNA molecules play a vital role in biological processes within the cell, with significant
implications for science and medicine. Notably, the biological functions exerted by specific …
implications for science and medicine. Notably, the biological functions exerted by specific …
Fine-tuning of the AMBER RNA force field with a new term adjusting interactions of terminal nucleotides
Determination of RNA structural-dynamic properties is challenging for experimental
methods. Thus, atomistic molecular dynamics (MD) simulations represent a helpful …
methods. Thus, atomistic molecular dynamics (MD) simulations represent a helpful …
Adjusting the energy profile for CH–O interactions leads to improved stability of RNA stem-loop structures in MD simulations
LE Raguette, SS Gunasekera… - The Journal of …, 2024 - ACS Publications
The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important
aspects of RNA behavior is lacking, such as dynamic structural ensembles in different …
aspects of RNA behavior is lacking, such as dynamic structural ensembles in different …
Conformational ensembles of noncoding elements in the SARS-CoV-2 genome from molecular dynamics simulations
S Bottaro, G Bussi… - Journal of the American …, 2021 - ACS Publications
The 5′ untranslated region (UTR) of the severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) genome is a conserved, functional and structured genomic region consisting …
(SARS-CoV-2) genome is a conserved, functional and structured genomic region consisting …