Interested in developing and applying new methods relating to free energy calculations? I have a postdoc position which just opened up in this area, working with OpenMM to advance binding free energy techniques and apply/validate them on problems relating to drug discovery. This is an NIH-funded project (1R01GM108889-01) and interfaces closely with other work going on in the group and elsewhere. [More…]
Guilherme Duarte Ramos Matos, Daisy Y. Kyu, Hannes H. Loeffler, John D. Chodera, Michael R. Shirts, David L. Mobley
Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review “alchemical” approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). [More…]
The special issue of JCAMD on the SAMPL5 distribution coefficient prediction challenge is out online now. If I understand correctly, all articles are open access for the first 30 days.
– David Mobley [More…]
I’m very excited to announce that I’m joining the scientific advisory board for OpenEye Scientific Software. We’ve collaborated with OpenEye extensively for many years, including work on the SAMPL series of blind challenges and publishing several papers together. We also use their awesome (and free for academics!) chemistry and modeling toolkits extensively in-house and as the basis for other software we work on such as our new Open Forcefield initiative, so strengthening this relationship makes a lot of sense. [More…]
We just released a new version of our “perpetual review” paper on benchmark sets for binding free energy calculations. This version adds new discussion on possible future benchmark sets, as well as on the need for workflow science. This paper is a bit of an experiment in publishing — we’re treating it sort of like software development, so it’s versioned, and we’re delighted to have community input, feedback, etc. [More…]