• 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 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 Alchemistry

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

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

News

Plans are coming together for the SAMPL6 challenge

Plans are starting to shape up for the SAMPL6 blind prediction challenge, coming later this year! (Our overall SAMPL initiative is still unfunded and we need your input, but we are able to proceed with SAMPL6).

SAMPL6 will focus on host-guest binding on some familiar systems, as well as logD prediction with known (provided) pKa values for a series of small organic compounds. [More…]

Posted: May 17, 2017 · Tags: Alchemistry, Benchmarks, Host-Guest Binding, LogD, LogP, SAMPL, pKa

News

SAMPL testimonials sought

For some time, we’ve been involved with running the SAMPL series of blind challenges focused on driving progress in modeling of physical properties and binding (see also the D3R page and our SAMPL NIH proposal) and recently, we’ve sought support from the NIH for this work. However, this is an unconventional type of proposal for the NIH, since the focus is on driving progress of other people’s methods.  [More…]

Posted: April 14, 2017 · Tags: Alchemistry, Grants, SAMPL

News

Postdoc position currently available (update: filled)

Interested in developing and applying new methods relating to free energy calculations? I have a postdoc position which just opened up in this area, working with OpenMM to advance binding free energy techniques and apply/validate them on problems relating to drug discovery. This is an NIH-funded project (1R01GM108889-01) and interfaces closely with other work going on in the group and elsewhere. [More…]

Posted: February 14, 2017 · Tags: Alchemistry, PostDoc

  • 1
  • 2
  • Next Page »

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 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...]

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...]

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:

  • Understanding Kinase Selectivity Through Energetic Analysis of Binding Site Waters April 16, 2021
  • Analysis of water patterns in protein kinase binding sites: Water Patterns in Protein Kinase Binding April 16, 2021
  • How Can Hydrophobic Association Be Enthalpy Driven? April 16, 2021
  • Molecular binding: Under water's influence April 16, 2021
  • Water Network Perturbation in Ligand Binding: Adenosine A <sub>2A</sub> Antagonists as a April 16, 2021

Archives

Tags

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

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