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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 147 43

  2. alchemical-analysis alchemical-analysis Public

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

    Python 122 59

  3. 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 110 19

  4. FreeSolv FreeSolv Public

    Experimental and calculated small molecule hydration free energies

    Python 109 53

  5. benchmarksets benchmarksets Public

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

    TeX 42 17

  6. Lomap Lomap Public archive

    Alchemical mutation scoring map

    Python 37 17

Repositories

Showing 10 of 56 repositories
  • 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 22 MIT 8 0 1 Updated Dec 4, 2024
  • ConformerDependentCharges Public
    MobleyLab/ConformerDependentCharges’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Nov 18, 2024
  • slow-rotations Public
    MobleyLab/slow-rotations’s past year of commit activity
    Python 2 MIT 0 0 0 Updated Oct 10, 2024
  • chemper Public

    Repository for Chemical Perception Sampling Tools

    MobleyLab/chemper’s past year of commit activity
    Python 19 MIT 10 16 (1 issue needs help) 1 Updated Aug 13, 2024
  • qm-theory-benchmark Public
    MobleyLab/qm-theory-benchmark’s past year of commit activity
    Jupyter Notebook 4 MIT 0 0 0 Updated Jul 9, 2024
  • mobleylab.org Public

    Lab website

    MobleyLab/mobleylab.org’s past year of commit activity
    SCSS 4 MIT 1 0 0 Updated Jul 8, 2024
  • alchemical-analysis Public

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

    MobleyLab/alchemical-analysis’s past year of commit activity
    Python 122 MIT 59 24 (2 issues need help) 4 Updated May 24, 2024
  • gmx_fileprep Public

    Scripts for local gromacs input file preparation

    MobleyLab/gmx_fileprep’s past year of commit activity
    1 0 0 1 Updated Apr 21, 2024
  • Training Public

    Lab policies, training, style guides, etc.

    MobleyLab/Training’s past year of commit activity
    35 MIT 5 0 1 Updated Apr 1, 2024
  • T4_MSM Public

    Code and files for analyzing the discrete conformational states of T4 L99A

    MobleyLab/T4_MSM’s past year of commit activity
    Jupyter Notebook 1 MIT 0 0 0 Updated Mar 8, 2024
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