• 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 Our science / Null results

Null results, Our science

Binding mode sampling: What didn’t work (that well)

One of the problems we have been very interested in over the years is the problem of ligand binding mode sampling, partly because we find that docking is good at generating plausible ligand binding modes that are stable for relatively long times in MD simulations, but bad at identifying which of these is best. We often then begin MD studies by clustering dock poses, taking members from many different clusters, and then running short MD simulations to identify which are stable. [More…]

Posted: June 2, 2017 ·

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

Tags

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

Contact

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

Meta

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

Copyright © 2019 · Education Pro Theme on Genesis Framework · WordPress · Log in