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@MobleyLab

Mobley Lab at UC Irvine

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

Popular repositories

  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 135 40

  2. alchemical-analysis alchemical-analysis Public

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

    Python 110 58

  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 102 17

  4. FreeSolv FreeSolv Public

    Experimental and calculated small molecule hydration free energies

    Python 95 53

  5. benchmarksets benchmarksets Public

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

    TeX 39 16

  6. Lomap Lomap Public archive

    Alchemical mutation scoring map

    Python 35 17

Repositories

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  • qm-theory-benchmark Public
    Jupyter Notebook 3 MIT 0 0 0 Updated May 14, 2024
  • T4_MSM Public

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

    Jupyter Notebook 0 MIT 0 0 0 Updated Mar 8, 2024
  • 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 135 CC-BY-4.0 40 8 0 Updated Feb 28, 2024
  • DEL_BB_design Public

    Computational enumeration of DNA-encoded libraries with various building block filtering and selection strategies

    Jupyter Notebook 1 1 0 0 Updated Jan 16, 2024
  • DEL_analysis Public

    Code to analyze the data from DNA-encoded libraries (DELs)

    Jupyter Notebook 8 MIT 1 0 0 Updated Jul 12, 2023
  • wbointerpolation Public

    Analysis scripts for the development of wiberg bond order interpolated parameters in the Open Force Field.

    Jupyter Notebook 3 MIT 3 0 4 Updated Jun 16, 2022
  • off-ffcompare Public

    Compare molecular structures after energy minimization in various force fields.

    Jupyter Notebook 9 7 8 0 Updated Aug 22, 2020
  • chemper_SI Public

    Using chemper to generate a protein SMIRNOFF with minimal human interference

    Jupyter Notebook 0 MIT 0 0 0 Updated Jun 21, 2019
  • SMIRNOFF_paper_code Public

    Code/tools relating to the initial SMIRNOFF format paper

    Jupyter Notebook 3 MIT 0 1 1 Updated Apr 25, 2019
  • IDAC_code Public
    Jupyter Notebook 0 0 0 0 Updated Nov 30, 2018
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