Proteins play a crucial role in organisms in nature. They are able to perform structural,
catalytic, transport and defense functions in cells, among others. We understand that a …

Highlights•Computational approaches are becoming an essential tool in modern drug
design.•Development of automated workflows from docking to MD techniques for drug …

The recent advances in relative protein–ligand binding free energy calculations have shown
the value of alchemical methods in drug discovery. Accurately assessing absolute binding …

Relative alchemical binding free energy calculations are routinely used in drug discovery
projects to optimize the affinity of small molecules for their drug targets. Alchemical methods …

Creating a successful small molecule drug is a challenging multiparameter optimization
problem in an effectively infinite space of possible molecules. Generative models have …

The capability to rank different potential drug molecules against a protein target for potency
has always been a fundamental challenge in computational chemistry due to its importance …

We apply the Alchemical Transfer Method (ATM) and a bespoke fixed partial charge force
field to the SAMPL9 bCD host–guest binding free energy prediction challenge that …

Decades of hardware, methodological, and algorithmic development have propelled
molecular dynamics (MD) simulations to the forefront of materials-modeling techniques …

We present a novel optimization approach to train a free-shape distance-dependent protein-
ligand scoring function called Convex-PL. We do not impose any functional form of the …

Drug discovery can be thought of as a search for a needle in a haystack: searching through
a large chemical space for the most active compounds. Computational techniques can …