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Mobley Lab, UCI

Free energy methods for pharmaceutical drug discovery

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News, Our science

Our SAMPL grant proposal revision is submitted

We’ve been helping to run the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) series of blind challenges for some time now, but the initiative is still unfunded. I’m excited that our revised grant proposal for the future of SAMPL has just been submitted to the NIH! While I normally wouldn’t post grant proposals, SAMPL is really a community resource, fueled by the community, so here’s a link to our plan for SAMPL’s future. [More…]

Posted: July 3, 2017 · Tags: Grants, SAMPL

News, Our science

Results of our SAMPL survey are out

We’re super excited about the Statistical Assessment of Modeling of Proteins and Ligand (SAMPL) series of blind challenges, and the potential these have for driving real advancements in modeling in our field. These challenges not only provide an opportunity for blind, prospective testing of our methods, but they also provide a crowdsourcing model to drive innovation. Such approaches have a well-documented history of spurring progress in specific areas, such as in the XPrize, the Netflix Prize, or, closer to our field, the DREAM challenges or CASP for protein structure prediction. [More…]

Posted: June 21, 2017 · Tags: Grants, SAMPL

News

SAMPL needs your input

We need your input on the future of the SAMPL series of blind challenges. Please use this SAMPL Google form to give us your thoughts on how helpful these challenges have been and on our plans for their future. Please also note that we need SAMPL testimonials.

– David L. Mobley [More…]

Posted: April 18, 2017 · Tags: Grants, SAMPL

News

SAMPL testimonials sought

For some time, we’ve been involved with running the SAMPL series of blind challenges focused on driving progress in modeling of physical properties and binding (see also the D3R page and our SAMPL NIH proposal) and recently, we’ve sought support from the NIH for this work. However, this is an unconventional type of proposal for the NIH, since the focus is on driving progress of other people’s methods.  [More…]

Posted: April 14, 2017 · Tags: Alchemistry, Grants, SAMPL

News

Winter 2016-2017 Highlights

Lab news and events:

Congratulations to graduate student Caitlin C. Bannan, who recently won the Penny J. Gilmer Grant for Women Graduate Students and Post-docs from OpenEye Scientific Software, AND the WCC Merck Research Award from the American Chemical Society!

We had about 20 middle school girls visit the lab on December 8 to learn about computational chemistry and intermolecular interactions as part of the Laboratory Experiments and Activities in the Physical Sciences (LEAPS) program at UCI, sponsored in part by our NSF CAREER award. [More…]

Posted: February 16, 2017 · Tags: FreeSolv, Grants, Highlights, PostDoc, Preprints, SAMPL

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Categories

  • Papers (12)
  • News (29)
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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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Contact

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

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