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Mobley Lab, UCI

Free energy methods for pharmaceutical drug discovery

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Our science

Music, instrument identification, and X-ray scattering

Check out this awesome YouTube video from graduate student David Wych on music, instrument identification, X-ray crystallography, and work we are doing relating to diffuse scattering. It’s definitely worth 3 minutes of your time!!

 

 

–  David L. Mobley [More…]

Posted: February 8, 2018 ·

News, Our science, Talks and posters

MiniCUP Presentation on BLUES

Last week I gave a presentation on our BLUES approach for ligand binding mode sampling at OpenEye’s San Diego MiniCUP presentation. Particular thanks are due to my students Nathan Lim (who did some real Keynote wizardry for these slides, which he gave a few weeks ago in London as well) and Sam Gill. Keynote slides (200+ MB) containing the  MiniCUP presentation are up; I’ve also posted a PDF version (no movies) on ResearchGate.
[More…]

Posted: November 16, 2017 ·

News, Our science

Binding modes of ligands using enhanced sampling – preprint

We have a new preprint up on our “Binding Modes of Ligands Using Enhanced Sampling” (BLUES) approach to sampling ligand binding modes. This is work with the Chodera lab, and applies the nonequilibrium candidate Monte Carlo technique to hop between different potential ligand binding modes, allowing us to compute the occupancy of ligand binding modes substantially more efficiently than with standard molecular dynamics or Monte Carlo. [More…]

Posted: September 21, 2017 · Tags: BLUES, Binding, Enhanced-sampling, binding modes

News, Our science

The SAMPL6 challenge kicks off!

Interested in predicting binding affinities? The SAMPL6 challenge is now live!

The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) series of blind challenges focuses on driving improvements in molecular modeling; in this sixth iteration of the challenge we have two new sets of host-guest binding data (from Gibb and Isaacs) for a new set of host-guest binding challenges. Additionally, we should shortly (thanks to Merck and the Chodera lab!) have new log D data for distribution coefficients. [More…]

Posted: August 28, 2017 · Tags: SAMPL, SAMPL6

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

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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:

  • Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Pr November 19, 2019
  • The translocation kinetics of antibiotics through porin OmpC: Insights from structure-based solvatio November 19, 2019
  • qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron November 19, 2019
  • A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0] November 19, 2019
  • NMR Characterization of Kinase p38 Dynamics in Free and Ligand-Bound Forms November 19, 2019

Archives

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

Contact

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

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