Free energy methods for pharmaceutical drug discovery
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Here, we focus on testing and improving force fields for molecular modeling, which see widespread use in diverse areas of computational chemistry and biomolecular simulation. [More…]
Check out these slides on Caitlin Bannan’s SAMPL6 blind challenge entry on pKa prediction! She spent her summer doing an internship at OpenEye building a machine learning model for pKa prediction, and entered it in the recent SAMPL6 blind prediction challenge. She just spoke today at the OpenEye CUP meeting in Santa Fe on the results, and these are her slides. [More…]
Samuel C. Gill, Nathan M. Lim, Patrick B. Grinaway, Ariën S. Rustenburg, Josh Fass, Gregory A. Ross, John D. Chodera and David L. Mobley
Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. [More…]
Check out this awesome YouTube video from graduate student David Wych on music, instrument identification, X-ray crystallography, and work we are doing relating to diffuse scattering. It’s definitely worth 3 minutes of your time!!
– David L. Mobley [More…]
The Open Forcefield Consortium [http://openforcefield.org] seeks a Lead Software Scientist to coordinate open source software development efforts for an interdisciplinary academic team developing next-generation molecular mechanics forcefields and associated parameterization infrastructure.
This exciting new initiative spans several academic institutions and will be supported by a pharmaceutical industry consortium, with potential for long-term support from the NIH and other agencies. [More…]