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Mobley Lab, UCI

Free energy methods for pharmaceutical drug discovery

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Presentations

Selected recent presentations:

  • “SAMPL: Its present and future, and some work on the logP challenge”, David Mobley, SAMPL/D3R workshop, August, 2019. (DOI)
  • “Machine Learning and pKa in SAMPL6”, Chodera lab seminar by Caitlin Bannan on YouTube.
  • “Molecular Dynamics Simulations of Protein X-ray Crystallographic Diffuse Scattering”, American Crystallographic Association Annual Meeting, Covington, KY, July 2019 (DOI)
  • “Infinite dilution activity coefficients… no, really, you should care!” OpenEye CUP Meeting, Santa Fe, NM, March 7, 2019. (DOI)
  • “OpenFF: Fitting of valence parameters,” Open Force Field Workshop, San Diego, CA, Jan. 9, 2019. (DOI)
  • “The Open Force Field Initiative: A brief update on our progress and plans,” OpenEye MiniCUP Meeting, San Diego, CA, Oct. 2, 2018. (DOI)
  • “Automated Chemical Perception for Force Field Parameterization”, 256th ACS National Meeting, Boston, MA, August 2018. (DOI)
  • “Learned chemical perception of force field typing rules using Monte Carlo sampling”, Inaugural Data Science Workshop, July 2018. (DOI)
  • “BLUES: Binding modes of Ligands Using Enhanced Sampling”, Computational Chemistry Gordon Research Seminar,  West Dover, VT, July 2018 (DOI, DOI).
  • “The BLUES Report”, OpenEye CUP CVIII Meeting, Santa Fe, NM, March 2018. (Link)
  • “Machine Learning and pKa Predictions in SAMPL6”, OpenEye CUP XVIII Meeting, Santa Fe, NM, March 2018. (DOI)
  • “Automating chemical perception to improve force field parameterization”, 254th ACS National Meeting, Washington, DC, August 2017. (DOI)
  • “Adapting free energy methods to predict binding modes of ligands”, CECAM workshop on “Beyond Kd’s: New computational methods to address challenges in drug discovery“, EPFL, Lausanne, Switzerland, June 7, 2017. (DOI)
  • “Making alchemical free energy calculations practical for drug discovery”, Pfizer WebEx presentation, April, 2017. (DOI)
  • “What happened when Ant let us put MD on Orion: Towards fragment binding occupancies using BLUES”, OpenEye CUP XVII Meeting, Santa Fe, NM, March 2017. (DOI)
  • “Improving Force Field Parameterization with Bayesian Inference for Chemical Perception”, OpenEye CUP XVII Meeting, Santa Fe, NM, March 2017. (DOI)
  • “Computing Partition Coefficients using Alchemical Free Energy Calculations”, 251st ACS National Meeting, San Diego, CA, March 2016. (DOI)

Older work which may still be helpful:

  • “Finite size artifacts” (charge corrections for alchemical free energy calculations), Dec.15, 2015, Gabriel Rocklin, via Hangouts on Air. Available on YouTube.

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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...]

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

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

Contact

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

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