• Home
  • Publications
  • Presentations
  • Research
  • Funding
  • Resources
  • People
    • Dr. David L. Mobley
    • PostDoc
      • Lea El Khoury
      • Sukanya Sasmal
    • Graduate
      • Sam Gill
      • Victoria Lim
      • Kalistyn Burley
      • David Wych
      • Danielle (Teresa) Bergazin
      • Jessica Maat
      • Hannah Baumann
      • Oanh Tran
    • Undergraduate
      • Meghan Osato
      • Jordan Ehrman

Mobley Lab, UCI

Free energy methods for pharmaceutical drug discovery

You are here: Home / Archives for FreeSolv

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

Papers

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

Guilherme Duarte Ramos Matos, Daisy Y. Kyu, Hannes H. Loeffler, John D. Chodera, Michael R. Shirts, David L. Mobley

Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review “alchemical” approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). [More…]

Posted: January 30, 2017 · Tags: Alchemistry, FreeSolv, Hydration, Papers

Research

One major emphasis is binding prediction

A major focus is the binding of small-molecule ligands to proteins. While current computational methods see widespread use in the pharmaceutical industry in drug discovery applications, accuracy is limited and these approaches fall far short of the goal of using computers to suggest new drug candidates. Methods we recently developed and applied have achieved far greater accuracies at computing and even predicting binding affinities than previous methods, so we are working to begin applying these in more complicated and pharmaceutically relevant binding sites. [More…]

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

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

Contact

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

Meta

  • Log in
  • Entries feed
  • Comments feed
  • WordPress.org
  • Home
  • Publications
  • Research
  • Funding
  • Resources
  • People
  • Presentations
  • Postdoc position with OpenFF
  • Oanh Tran

Copyright © 2021 · Education Pro on Genesis Framework · WordPress · Log in