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Mobley Lab, UCI

Free energy methods for pharmaceutical drug discovery

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Postdoc position with OpenFF

The Open Force Field Initiative is seeking a talented postdoctoral fellow to work on the development of next-generation molecular mechanics force fields, initially focusing on the development of open source tools for generating QM-derived torsion parameters for small organic molecules. The position is supported by the Open Force Field Consortium, which is administered by the NSF-funded Molecular Sciences Software Institute (MolSSI) and funded by an alliance of pharmaceutical and biotech companies aiming to advance the state of force fields for biomolecular simulation and design through an open collaborative effort.

The Open Force Field Initiative is a multi-investigator collaboration that aims to build new, quantitatively accurate molecular mechanics force fields supported by a modern software infrastructure, built on principles of open source, open data, and open science.

Desired qualifications:

  • Experience with the theory and practice of atomistic biomolecular simulation using molecular mechanics force fields
  • Comfortable with the Python programming language
  • Exposure to modern open source software development practices (GitHub, unit tests, continuous integration)
  • Good multidisciplinary teamwork and communication skills

Bonus qualifications (nice to have, but not required!):

  • Experience with force field parameter fitting for small organic molecules
  • Experience with quantum chemical calculations in general, and psi4 in particular
  • Experience with high-performance computing clusters and/or cloud computing
  • Knowledge of organic chemistry
  • Experience with the open-source GPU-accelerated molecular simulation Python library OpenMM
  • Experience with probabilistic programming languages (e.g. PyMC, tensorflow.Probability, Pyro) and/or machine learning frameworks like TensorFlow
  • Experience with cheminformatics or computer-aided drug discovery

Location: Choice of location is flexible, with potential sites including the participating investigator laboratories: Michael K. Gilson (UCSD, La Jolla, CA), John D. Chodera (MSKCC, New York City, NY), Lee-Ping Wang (UCD, Davis, CA), David L. Mobley (UCI, Irvine, CA), or Michael R. Shirts (University of Colorado, Boulder, CO).

Appointment: The initial appointment will be for one year, with the potential for extension to multiple years to focus on other aspects of force field science and engineering. Position is pending final approval of funding.

Open Force Field Initiative: To find out more about the Open Force Field Initiative, visit http://openforcefield.org.

Application: Interested candidates should send an application to openforcefield@choderalab.org (cc dmobley@uci.edu) with the subject line “Bespoke Torsions Postdoc application” that includes:
• a cover letter explaining your motivation, background, and qualifications for the position
• a detailed Curriculum Vitae (including a list of publications)
• contact information of at least two references

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Posted: November 12, 2018 · Tags: Open Force Field, PostDoc

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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:

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  • 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

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Contact

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

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