Y Miao, VA Feher, JA McCammon - Journal of chemical theory …, 2015 - ACS Publications
A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost …
Despite recent advances in the development of machine learning potentials (MLPs) for biomolecular simulations, there has been limited effort on developing stable and accurate …
The SARS-CoV-2 coronavirus is an enveloped, positive-sense single-stranded RNA virus that is responsible for the COVID-19 pandemic. The spike is a class I viral fusion …
Gaussian accelerated molecular dynamics (GaMD) is a recently developed enhanced sampling technique that provides efficient free energy calculations of biomolecules. Like the …
BP Brown, RA Stein, J Meiler… - Journal of Chemical …, 2024 - ACS Publications
Protein thermodynamics is intimately tied to biological function and can enable processes such as signal transduction, enzyme catalysis, and molecular recognition. The relative free …
Flavodiiron proteins possess reductive scavenging properties toward dioxygen and/or nitric oxide in various microorganisms. Among them, the Desulfovibrio gigas flavodiiron protein …
Magnesium ions play an essential role in many vital processes. To correctly describe their interactions in molecular dynamics simulations, an accurate parametrization is crucial …
J Zhang, Y Cong, L Duan… - Journal of Chemical …, 2023 - ACS Publications
The Omicron lineage of SARS-CoV-2, which was first reported in November 2021, has spread globally and become dominant, splitting into several sublineages. Experiments have …
Developing accurate classical force field representations of molecules is key to realizing the full potential of molecular simulations, both as a powerful route to gaining fundamental …