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Mobley Lab, UCI

Free energy methods for pharmaceutical drug discovery

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Mobley lab highlights for 2019

We’ve had a busy year, with lots of significant accomplishments and new directions, as well as several new Ph.D.’s!

Graduations:

  • 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).

Rotation students:

  • Trevor Gokey, an incoming Chem. student, is rotating in the lab

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Related

Posted: August 17, 2019 ·

Categories

  • Papers (12)
  • News (29)
  • Commentary (1)
  • Meetings and workshops (1)
  • Null results (1)
  • Our science (12)
  • Positions (4)
  • Talks and posters (4)

People

  • Dr. David L. Mobley
  • PostDoc
    • Lea El Khoury
    • Sukanya Sasmal
  • Graduate
    • Sam Gill
    • Victoria Lim
    • Kalistyn Burley
    • David Wych
    • Jessica Maat
    • Danielle (Teresa) Bergazin
    • Hannah Baumann
    • Oanh Tran
  • Undergraduate
    • Meghan Osato
    • Jordan Ehrman

Recent Papers

Escaping Atom Types in Force Fields Using Direct Chemical Perception

David L. Mobley , Caitlin C. Bannan , Andrea … [Read More...]

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules

Guilherme Duarte Ramos Matos, David L. … [Read More...]

SAMPL6 challenge results from pKa predictions based on a general Gaussian process model

Caitlin C. Bannan, David L. Mobley, A. Geoffrey … [Read More...]

Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1

David Mobley, Caitlin C. Bannan, Andrea Rizzi, … [Read More...]

Binding modes of ligands using enhanced sampling (BLUES)

Samuel C. Gill, Nathan M. Lim, Patrick B. … [Read More...]

RSS What we’re reading:

  • A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums November 25, 2020
  • Characterization of the TIP4P-Ew water model: Vapor pressure and boiling point November 25, 2020
  • Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew November 25, 2020
  • A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modif November 25, 2020
  • The missing term in effective pair potentials November 25, 2020

Archives

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PostDoc Benchmarks Undergraduate Open Force Field Papers SAMPL Graduate Alchemistry Grants Binding

Contact

David L. Mobley
dmobley@mobleylab.org
phone: 949.385.2436
office: 3134B Nat. Sci. I

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