Lipid21: complex lipid membrane simulations with AMBER

CJ Dickson, RC Walker, IR Gould - Journal of chemical theory and …, 2022 - ACS Publications
We extend the modular AMBER lipid force field to include anionic lipids, polyunsaturated
fatty acid (PUFA) lipids, and sphingomyelin, allowing the simulation of realistic cell …

Gaussian accelerated molecular dynamics: unconstrained enhanced sampling and free energy calculation

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 …

Machine-learning-assisted free energy simulation of solution-phase and enzyme reactions

X Pan, J Yang, R Van, E Epifanovsky, J Ho… - Journal of chemical …, 2021 - ACS Publications
Despite recent advances in the development of machine learning potentials (MLPs) for
biomolecular simulations, there has been limited effort on developing stable and accurate …

Free energy landscapes from SARS-CoV-2 spike glycoprotein simulations suggest that RBD opening can be modulated via interactions in an allosteric pocket

L Fallon, KAA Belfon, L Raguette, Y Wang… - Journal of the …, 2021 - ACS Publications
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 in NAMD

YT Pang, Y Miao, Y Wang… - Journal of chemical …, 2017 - ACS Publications
Gaussian accelerated molecular dynamics (GaMD) is a recently developed enhanced
sampling technique that provides efficient free energy calculations of biomolecules. Like the …

Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations

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 …

Computational Exploration of Enzyme Promiscuity: Mechanisms of O2 and NO Reduction Activities of the Desulfovibrio gigas Flavodiiron Protein

WH Deng, TP Zhou, RZ Liao - ACS Catalysis, 2023 - ACS Publications
Flavodiiron proteins possess reductive scavenging properties toward dioxygen and/or nitric
oxide in various microorganisms. Among them, the Desulfovibrio gigas flavodiiron protein …

Optimized magnesium force field parameters for biomolecular simulations with accurate solvation, ion-binding, and water-exchange properties

KK Grotz, S Cruz-León, N Schwierz - Journal of chemical theory …, 2021 - ACS Publications
Magnesium ions play an essential role in many vital processes. To correctly describe their
interactions in molecular dynamics simulations, an accurate parametrization is crucial …

Combined antibodies evusheld against the sars-cov-2 omicron variants ba. 1.1 and ba. 5: immune escape mechanism from molecular simulation

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 …

Open force field evaluator: An automated, efficient, and scalable framework for the estimation of physical properties from molecular simulation

S Boothroyd, LP Wang, DL Mobley… - Journal of chemical …, 2022 - ACS Publications
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 …