Molecular docking has become an important component of the drug discovery process.
Since first being developed in the 1980s, advancements in the power of computer hardware …

Conspectus In structure-based drug design, scoring functions are widely used for fast
evaluation of protein–ligand interactions. They are often applied in combination with …

The 2014 CSAR Benchmark Exercise was the last community-wide exercise that was
conducted by the group at the University of Michigan, Ann Arbor. For this event …

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 …

Motivation Docking prediction algorithms aim to find the native conformation of a complex of
proteins from knowledge of their unbound structures. They rely on a combination of …

Abstract The 2016 D3R Grand Challenge 2 provided an opportunity to test multiple protein–
ligand docking protocols on a set of ligands bound to farnesoid X receptor that has many …

Abstract The D3R Grand Challenge 4 provided a brilliant opportunity to test macrocyclic
docking protocols on a diverse high-quality experimental data. We participated in both pose …

In the design of high-affinity and enzyme isoform-selective inhibitors, we applied an
approach of augmenting the substituents attached to the benzenesulfonamide scaffold in …

Abstract The 2015 D3R Grand Challenge provided an opportunity to test our new model for
the binding free energy of small molecules, as well as to assess our protocol to predict …

Drug discovery is a very expensive process consisting of multiple phases. Computer
simulations provide an opportunity to scale and speed up its early stages by performing the …