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@MobleyLab

Mobley Lab at UC Irvine

Binding free energies, molecular interactions, solvation thermodynamics, and statistical mechanics of biomolecules

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  1. drug-computing drug-computing Public

    Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.

    Jupyter Notebook 151 43

  2. alchemical-analysis alchemical-analysis Public

    An open tool implementing some recommended practices for analyzing alchemical free energy calculations

    Python 126 60

  3. FreeSolv FreeSolv Public

    Experimental and calculated small molecule hydration free energies

    Python 116 53

  4. basic_simulation_training basic_simulation_training Public

    A document for the Living Journal of Computational Molecular Science (LiveCoMS) which describes basic training for molecular simulations (oriented towards molecular dynamics (MD)), providing some t…

    TeX 114 19

  5. benchmarksets benchmarksets Public

    Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards

    TeX 43 18

  6. Lomap Lomap Public archive

    Alchemical mutation scoring map

    Python 37 17

Repositories

Showing 10 of 56 repositories
  • blues Public

    Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling

    Python 33 MIT 16 14 (6 issues need help) 7 Updated Mar 22, 2025
  • drug-computing Public

    Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.

    Jupyter Notebook 151 CC-BY-4.0 43 8 0 Updated Mar 11, 2025
  • mobleylab.org Public

    Lab website

    SCSS 4 MIT 1 0 0 Updated Feb 12, 2025
  • slow-rotations Public
    Python 2 MIT 0 0 0 Updated Jan 28, 2025
  • SeparatedTopologies Public

    Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).

    Python 24 MIT 8 1 1 Updated Dec 4, 2024
  • ConformerDependentCharges Public
    Jupyter Notebook 2 MIT 1 0 0 Updated Nov 18, 2024
  • chemper Public

    Repository for Chemical Perception Sampling Tools

    Python 20 MIT 10 16 (1 issue needs help) 1 Updated Aug 13, 2024
  • qm-theory-benchmark Public
    Jupyter Notebook 4 MIT 1 0 0 Updated Jul 9, 2024
  • alchemical-analysis Public

    An open tool implementing some recommended practices for analyzing alchemical free energy calculations

    Python 126 MIT 60 24 (2 issues need help) 3 Updated May 24, 2024
  • gmx_fileprep Public

    Scripts for local gromacs input file preparation

    1 0 0 1 Updated Apr 21, 2024
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