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Mobley Lab, UCI

Free energy methods for pharmaceutical drug discovery

News, Positions

Recent lab highlights

I’m behind on updates,but there’s a lot of great news recently! Here are some highlights.

Lab news and events:

First year graduate students Danielle Bergazin, Jessica Maat and Noora Siddiqui recently joined the lab. This is in addition to a rotation by Daniel Seith.

We also have great news on the funding front — huge congratulations to Noora, who was just awarded a prestigious DOE CSGF to support her graduate studies! [More…]

Posted: April 6, 2018 ·

Papers, Our science

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

David Mobley, Caitlin C. Bannan, Andrea Rizzi, Christopher I. Bayly, John D. Chodera, Victoria T Lim, Nathan M. Lim, Kyle A. Beauchamp, Michael R. Shirts, Michael K. Gilson, and Peter K. Eastman

 

 

Here, we focus on testing and improving force fields for molecular modeling, which see widespread use in diverse areas of computational chemistry and biomolecular simulation. [More…]

Posted: March 24, 2018 · Tags: Open Force Field, Software

Our science, Talks and posters

Machine learning and pKa prediction in SAMPL6

Check out these slides on Caitlin Bannan’s SAMPL6 blind challenge entry on pKa prediction! She spent her summer doing an internship at OpenEye building a machine learning model for pKa prediction, and entered it in the recent SAMPL6 blind prediction challenge. She just spoke today at the OpenEye CUP meeting in Santa Fe on the results, and these are her slides. [More…]

Posted: March 7, 2018 · Tags: SAMPL, SAMPL6, pKa

Papers

Binding modes of ligands using enhanced sampling (BLUES)

BLUES enhances samling of ligand binding modes

Samuel C. Gill, Nathan M. Lim, Patrick B. Grinaway, Ariën S. Rustenburg, Josh Fass, Gregory A. Ross, John D. Chodera and David L. Mobley

 

 

Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments.  [More…]

Posted: February 28, 2018 · Tags: Alchemistry, BLUES, Binding, Papers

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 ·

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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...]

Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides

Z. A. Könst, A. R. Szklarski, S. Pellegrino, S. E. … [Read More...]

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database

Guilherme Duarte Ramos Matos, Daisy Y. Kyu, Hannes … [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

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

Contact

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

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