Woody Sherman

TL;DR: It is shown that database enrichment is improved with proper preparation and that neglecting certain steps of the preparation process produces a systematic degradation in enrichments, which can be large for some targets.

TL;DR: A novel protein-ligand docking method that accurately accounts for both ligand and receptor flexibility by iteratively combining rigid receptor docking (Glide) with protein structure prediction (Prime) techniques is presented.

TL;DR: This work uses explicit solvent molecular dynamics free energy perturbation to predict the absolute solvation free energies of a set of 239 small molecules, spanning diverse chemical functional groups commonly found in drugs and drug-like molecules and shows that predictions can be improved by using a semiempirical charge assignment method with an implicit bond charge correction.

TL;DR: The optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.

TL;DR: An approach to designing tight-binding ligands with a substantial reduction in false positives relative to compounds synthesized on the basis of other computational or medicinal chemistry approaches is reported, demonstrating the robustness and broad range of applicability of this approach, which can be used to drive decisions in lead optimization.