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Mobley Lab, UCI

Free energy methods for pharmaceutical drug discovery

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We had a great last year with four graduate students joining the lab and four graduating! Welcome Hannah, Martin, Chris and Tran! Congratulations to Guilherme, Camilla, Caitlin and Nathan!

News

Postdoc position available in the Mobley lab

Interested in improving predictive modeling of biomolecular interactions? We seek a postdoc who will work on binding free energy methods and applications (likely including our BLUES method for enhanced sampling of ligand binding modes), as well as with the Open Force Field Initiative (OpenFF, openforcefield.org) on testing and improving biomolecular force fields, though this is not an OpenFF position. The candidate may also get involved with the SAMPL series of blind challenges, helping to drive progress in the field by facilitating comparisons of the latest methods on cutting-edge datasets in blind challenges we help design. [More…]

Posted: November 18, 2019 · Tags: PostDoc, jobs

News

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.
[More…]

Posted: August 17, 2019 ·

News

Postdoc position available on free energy calculations

Interested in developing and applying new methods relating to binding free energy calculations, and in advancing predictive modeling relating to pharmaceutical drug discovery? I seek a postdoctoral candidate who will focus on methods for and applications of free energy calculations and structure-based design methods in early stage drug discovery projects. Additionally, the candidate will likely get involved with the SAMPL series of blind challenges, helping to drive progress in the field by facilitating comparisons of the latest methods on cutting-edge datasets in blind challenges we help design. [More…]

Posted: April 5, 2019 · Tags: PostDoc

News

Mobley lab highlights since Spring

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.
[More…]

Posted: November 12, 2018 ·

News, Our science

The Open Force Field Consortium launches; check out a webinar

We’re very excited about the Open Force Field Initiative, a new effort to help build better force fields and improve the infrastructure for developing them. And we’re especially excited that a pharmaceutical industry consortium has come together to help fund and guide this work. Check out our announcement for more details!

If you’d like to know more about our longer-term plans, check out graduate student Caitlin Bannan’s upcoming BioExcel Webinar Oct. [More…]

Posted: October 6, 2018 ·

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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

Tags

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

Contact

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

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