Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for
simultaneous unconstrained enhanced sampling and free energy calculations of …

Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently
could provide reliable answers to questions pertaining to the structure-function relationship …

NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently needs an effective cure. 3CL …

TCR-signaling strength generally correlates with peptide-MHC binding affinity; however,
exceptions exist. We find high-affinity, yet non-stimulatory, interactions occur with high …

Calculations of ligand binding free energies and kinetic rates are important for drug design.
However, such tasks have proven challenging in computational chemistry and biophysics …

The chemokine receptor CCR5 plays a vital role in immune surveillance and inflammation.
However, molecular details that govern its endogenous chemokine recognition and receptor …

Biomolecular binding kinetics including the association (k on) and dissociation (k off) rates
are critical parameters for therapeutic design of small-molecule drugs, peptides, and …

Peptides mediate up to 40% of known protein–protein interactions in higher eukaryotes and
play an important role in cellular signaling. However, it is challenging to simulate both …

Complete understanding of most, if not all chemical processes requires at its very core the
knowledge of the underlying free-energy change. In computer-aided drug design, for …