Highlights•Currently, developing a market-approved drug costs a staggering $2.6 billion.•In
silico methods have become an important strategy for narrowing down on promising lead …

Interactions between proteins are orchestrated in a precise and time-dependent manner,
underlying cellular function. The binding affinity, defined as the strength of these …

We present a robust and efficient method to implicitly account for solvation effects in modern
semiempirical quantum mechanics and force fields. A computationally efficient yet accurate …

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) has become a global crisis. There is no therapeutic treatment specific for …

We present an implementation of explicit solvent all atom classical molecular dynamics (MD)
within the AMBER program package that runs entirely on CUDA-enabled GPUs. First …

We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely
available computer programs for the analysis and processing of time series of three …

Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …

Accurate prediction of binding affinities has been a central goal of computational chemistry
for decades, yet remains elusive. Despite good progress, the required accuracy for use in a …

The increasing availability of high-quality experimental data and first-principles calculations
creates opportunities for developing more accurate empirical force fields for simulation of …

Elucidating details of the relationship between molecular structure and a particular
biological end point is essential for successful, rational drug discovery. Molecular docking is …