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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 165 44

  2. FreeSolv FreeSolv Public

    Experimental and calculated small molecule hydration free energies

    Python 135 55

  3. alchemical-analysis alchemical-analysis Public

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

    Python 135 62

  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 118 19

  5. benchmarksets benchmarksets Public

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

    TeX 47 18

  6. Lomap Lomap Public archive

    Alchemical mutation scoring map

    Python 41 17

Repositories

Showing 10 of 59 repositories
  • active-learning-notebooks Public

    Jupyter notebooks for ligand optimization studies involving active learning

    MobleyLab/active-learning-notebooks’s past year of commit activity
    Jupyter Notebook 5 MIT 2 1 0 Updated Feb 8, 2026
  • slow-rotations-systems Public

    Input files used for simulations to test slow-rotations

    MobleyLab/slow-rotations-systems’s past year of commit activity
    Shell 1 0 0 0 Updated Jan 15, 2026
  • mobleylab.org Public

    Lab website

    MobleyLab/mobleylab.org’s past year of commit activity
    SCSS 4 MIT 1 0 0 Updated Jan 6, 2026
  • Training Public

    Lab policies, training, style guides, etc.

    MobleyLab/Training’s past year of commit activity
    35 MIT 5 0 1 Updated Dec 9, 2025
  • blues Public

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

    MobleyLab/blues’s past year of commit activity
    Python 34 MIT 16 15 (6 issues need help) 6 Updated Nov 12, 2025
  • ssBind Public Forked from suleymanselim/ssBind
    MobleyLab/ssBind’s past year of commit activity
    Python 0 MIT 2 0 0 Updated Nov 10, 2025
  • slow-rotations Public

    readthedocs

    MobleyLab/slow-rotations’s past year of commit activity
    Python 6 MIT 0 0 0 Updated Oct 27, 2025
  • waterNES Public

    Workflows to calculate relative free energies using non-equilibrium switching for buried water molecules

    MobleyLab/waterNES’s past year of commit activity
    Python 4 MIT 0 0 0 Updated Jun 7, 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.

    MobleyLab/drug-computing’s past year of commit activity
    Jupyter Notebook 165 CC-BY-4.0 44 8 0 Updated Mar 11, 2025
  • SeparatedTopologies Public

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

    MobleyLab/SeparatedTopologies’s past year of commit activity
    Python 28 MIT 9 2 1 Updated Dec 4, 2024
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