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…]
Binding modes of ligands using enhanced sampling (BLUES)
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…]
Music, instrument identification, and X-ray scattering
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 seeks a software scientist
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…]
Announcing the Living Journal of Computational Molecular Science
A modern journal paradigm for molecular simulation:
Open access, nonprofit, low cost, and updateable
The Living Journal of Computational Molecular Science (LiveCoMS) is a peer-reviewed, ultra-low-cost, open-access journal that invites your submissions. LiveCoMS seeks to bring publication of educational, review, and best practices materials into the modern age, allowing authors to publish their work but then continue its development. LiveCoMS also attempts to better align academic incentives with the realities of computational work that require development of community resources. [More…]
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