We’ve had a busy year, with lots of significant accomplishments and new directions, as well as several new Ph.D.’s!
- Camila Zanette finished her Ph.D. and went on to work in bioinformatics in the Irvine area.
- Caitlin Bannan finished her Ph.D. and went on to a position at OpenEye Scientific Software
- Guilherme Duarte Ramos Matos received his Ph.D. and is joining the Rizzo Lab at Stony Brook University for a postdoc position.
- Nathan Lim finished his Ph.D. and is joining Janssen Pharmaceuticals in San Diego as a postdoc.
Other lab news and events:
- Victoria Lim spent Summer 2019 on an exchange program with Eric Lindahl in Sweden
- Kalistyn Burley spent Summer 2019 on an internship at Vertex
- David Wych is spending a significant chunk of 2019 with Mike Wall at Los Alamos
- First-year student Martin Amezcua received a fellowship from the NIH to help extend the SAMPL series of challenges in a new direction
New publications and preprints:
- We’ve got a new preprint utilizing results of the OpenFF initiative for host-guest binding: DOI.
- Work on automated chemical perception for OpenFF is described in Bannan’s new preprint: DOI
- We participated in the recent D3R grand challenge examining BACE inhibition, and our work on binding prediction is described here: DOI. A second study, examining how MM-GBSA aided docking, is also up here: DOI
- With Pfizer, we examined alternative ways of laying out maps of relative free energy calculations for greater efficiency: DOI.
- We used our BLUES technique to examine binding modes of caffeine to understand its metabolism; this work, with Zuzana Jandova and Chris Oostenbrink, is out in Chem. Res. Toxicol. 32(7):1374-1383 (2019). (Paper: DOI).
- With Chris Vanderwal’s group, follow-up worked provided new insights into how the lissoclimides interact with the ribosome: Nucleic Acids Research 47(6):3223-3232 (2019). (Paper: DOI).
- A new study examines how experiments and computation can reveal solvation structure around biomolecules: J. Am. Chem. Soc. 141(11);4711-4720 (2019). (Preprint: DOI ; paper DOI)
- Our BLUES technique also proves useful for enhancing sidechain sampling in proteins, J. Chem. Theory Comput. 15(3):1848-1862 (2019). (preprint DOI, publication DOI)
- A combined QM and MM study provides insight into conformational equilibria of carboxylic acids and how this is modulated by solvent: J. Chem. Inf. Model. (DOI).
- Trevor Gokey, an incoming Chem. student, is rotating in the lab