Free energy methods for pharmaceutical drug discovery
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…]
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…]
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…]
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…]