INTRODUCTION The eukaryotic nucleus pro-tects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ...
The journal of physical chemistry letters
May 6, 2022
molecular dynamics (AIMD) is an established method for revealing the reactive dynamics of complex systems. However, the high computational cost of AIMD restricts the explorable length and time scales. Here, we develop a fundamentally different appro...
This work presents Neural Equivariant Interatomic Potentials (NequIP), an E(3)-equivariant neural network approach for learning interatomic potentials from ab-initio calculations for molecular dynamics simulations. While most contemporary symmetry-aw...
Journal of chemical information and modeling
Apr 14, 2022
Graph neural network (GNN)-based deep learning (DL) models have been widely implemented to predict the experimental aqueous solvation free energy, while its prediction accuracy has reached a plateau partly due to the scarcity of available experimenta...
Journal of chemical theory and computation
Apr 6, 2022
An effective implementation of enhanced sampling algorithms for molecular dynamics simulations requires knowledge of the approximate reaction coordinate describing the relevant mechanisms in the system. In this work, we focus on the recently develop...
Journal of chemical information and modeling
Mar 30, 2022
Conformational sampling of protein structures is essential for understanding biochemical functions and for predicting thermodynamic properties such as free energies. Where previous approaches rely on sequential sampling procedures, recent development...
Journal of chemical theory and computation
Mar 11, 2022
Computing accurate reaction rates is a central challenge in computational chemistry and biology because of the high cost of free energy estimation with unbiased molecular dynamics. In this work, a data-driven machine learning algorithm is devised to ...
Journal of chemical information and modeling
Mar 8, 2022
Molecular dynamics (MD) simulations have made great contribution to revealing structural and functional mechanisms for many biomolecular systems. However, how to identify functional states and important residues from vast conformation space generated...
Since December 2019, SARS-CoV-2 has continued to spread rapidly around the world. The effective drugs may provide a long-term strategy to combat this virus. The main protease (Mpro) and papain-like protease (PLpro) are two important targets for the ...