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Mobley Lab, UCI

Free energy methods for pharmaceutical drug discovery

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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 ·

Papers, Our science

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

Guilherme Duarte Ramos Matos, David L. Mobley

Background: Solubility is a physical property of high importance to the pharmaceutical industry, the prediction of which for potential drugs has so far been a hard task. We attempted to predict the solubility of acetylsalicylic acid (ASA) by estimating the absolute chemical potentials of its most stable polymorph and of solutions with different concentrations of the drug molecule.
[More…]

Posted: June 6, 2018 · Tags: Alchemistry, solubility

Papers, Our science

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

Caitlin C. Bannan, David L. Mobley, A. Geoffrey Skillman

A variety of fields would benefit from accurate pKa predictions, especially drug design due to the affect a change in ionization state can have on a molecules physiochemical properties. Participants in the recent SAMPL6 blind challenge were asked to submit predictions for microscopic and macroscopic pKas of 24 drug like small molecules. 
[More…]

Posted: June 6, 2018 · Tags: machine learning, pKa

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

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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...]

Binding modes of ligands using enhanced sampling (BLUES)

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

Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

Stefania Evoli, David L. Mobley, Rita Guzzi and … [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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Undergraduate Open Force Field Graduate Grants Alchemistry Binding Benchmarks SAMPL Papers PostDoc

Contact

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

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