There’s lots of great news since my last update in April.
Lab news and events:
- New graduate student Hannah Baumann recently joined the lab, coming to us from Germany after an internship at Merck Group doing free energy calculations. She’s probably done more such calculations than anyone in the lab!
- Rotation students Martin Amezcua, Oanh Tran, Chris Zhang and Ellie Frank are spending time in the lab this quarter
- Caitlin Bannan received an NSF MolSSI Phase II Fellowship for her work on direct chemical perception with the Open Force Field Initiative
- Nathan Lim was awarded an NSF MolSSI Phase I Fellowship for his work on our BLUES software package.
- Danielle Bergazin was awarded an ACM SIGHPC and Intel Computational and Data Science fellowship.
- Sam Gill returned from a summer internship at GSK in Philadelphia
- Caitlin Bannan returned from a summer internship at OpenEye Scientific Software in Santa Fe, NM
- We welcome Jeff Wagner, a postdoc/software scientist with the Open Force Field Initiative who is based in our group.
- Our first paper on the Open Force Field Initiative and our new small molecule force field is out in JCTC
- Our SAMPL6 pKa measurements work is out in JCAMD
- The SAMPL6 host-guest overview paper is out in JCAMD
- Our work on a machine learning model for predicting pKa’s in SAMPL6 is out in JCAMD
- Work we did with our visitor, Max Troncoso, and his supervisor Esteban Vohringer-Martinez, on small molecule hydration free energies is out in JCIM.
- We finished a lengthy study on reproducibility of relative hydration free energy calculations, out in JCTC.
- We have a new preprint out on using infinite dilution activity coefficients to test force fields
- … and another new preprint on using BLUES to enhance sidechain sampling on ligand binding
- Our “basic simulation training” best practices paper was just accepted by the Living Journal of Computational Molecular Science (LiveCoMS), and you can see the preprint/latest version on GitHub. On that note we’re also very excited that the first issue of LiveCoMS is coming out shortly!
SAMPL grant awarded:
We recently got word that that the NIH will support our work on the SAMPL series of blind prediction challenges, a community resource designed to drive progress in predictive modeling. This will allow us to field a series of challenges focused on prediction of physical properties, binding in model systems, and even extending to protein-ligand binding. Currently we are fielding a “SAMPL6 part 2” challenge (see github.com/mobleylab/sampl6) on logP prediction, but stay tuned for news of more challenges to come as we get the NIH-funded work up and running!
Positions in the Open Force Field Initiative:
The Open Force Field Consortium (openforcefield.org) is hiring a postdoc to work on torsion fitting, to be situated in one of the participating academic labs, including potentially at UCI.