We’ve been working on planning future iterations of the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges, and have given a lot of thought to how to design SAMPL challenges in order to systematically advance predictive modeling for pharmaceutical drug discovery and molecular design. In our view, we need a series of blind predictive challenges specifically tailored to focus on the major challenges impairing accuracy. [More…]
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David L. Mobley has submitted a review paper on benchmark sets for binding free energy calculations titled Predicting binding free energies: Frontiers and benchmarks to bioRxiv and Annual Reviews in Biophysics. Check out the related Github repo for more info. [More…]
Nathan M. Lim, Lingle Wang, Robert Abel, and David L. Mobley
Tremendous recent improvements in computer hardware, coupled with advances in sampling techniques and force fields, are now allowing protein–ligand binding free energy calculations to be routinely used to aid pharmaceutical drug discovery projects. However, despite these recent innovations, there are still needs for further improvement in sampling algorithms to more adequately sample protein motion relevant to protein–ligand binding. [More…]
Caitlin C. Bannan, Gaetano Calabró, Daisy Y. Kyu, and David L. Mobley
Partition coefficients describe how a solute is distributed between two immiscible solvents. They are used in drug design as a measure of a solute’s hydrophobicity and a proxy for its membrane permeability. We calculate partition coefficients from transfer free energies using molecular dynamics simulations in explicit solvent. [More…]