Last week I gave a presentation on our BLUES approach for ligand binding mode sampling at OpenEye’s San Diego MiniCUP presentation. Particular thanks are due to my students Nathan Lim (who did some real Keynote wizardry for these slides, which he gave a few weeks ago in London as well) and Sam Gill. Keynote slides (200+ MB) containing the MiniCUP presentation are up; I’ve also posted a PDF version (no movies) on ResearchGate. [More…]
2018 Workshop on Free Energy Methods
We’re super excited that the 2018 Workshop on Free Energy Methods is coming together for May, 2018, at Novartis in Cambridge, MA! I’ve really enjoyed this workshop over the years — it’s been a great opportunity to see the field, grow, mature, and shift from a meeting where there are a lot of spectators from the pharmaceutical industry who hope these calculations might eventually be of use, to one where we get to hear about the latest applications, challenges, and successes in industrial applications. [More…]
Binding modes of ligands using enhanced sampling – preprint
We have a new preprint up on our “Binding Modes of Ligands Using Enhanced Sampling” (BLUES) approach to sampling ligand binding modes. This is work with the Chodera lab, and applies the nonequilibrium candidate Monte Carlo technique to hop between different potential ligand binding modes, allowing us to compute the occupancy of ligand binding modes substantially more efficiently than with standard molecular dynamics or Monte Carlo. [More…]
Undergraduate research position available
We have an undergraduate research position available applying computer tools to help identify candidate drug molecules for experimental testing using docking and screening techniques, working with experimental collaborators. Please use this form if you may be interested. [More…]
The SAMPL6 challenge kicks off!
Interested in predicting binding affinities? The SAMPL6 challenge is now live!
The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) series of blind challenges focuses on driving improvements in molecular modeling; in this sixth iteration of the challenge we have two new sets of host-guest binding data (from Gibb and Isaacs) for a new set of host-guest binding challenges. Additionally, we should shortly (thanks to Merck and the Chodera lab!) have new log D data for distribution coefficients. [More…]
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