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    • readthedocs
      Python
      MIT License
      0600Updated Apr 8, 2026Apr 8, 2026
    • FreeSolv

      Public
      Experimental and calculated small molecule hydration free energies
      Python
      Creative Commons Attribution 4.0 International
      56137171Updated Apr 3, 2026Apr 3, 2026
    • waterNES

      Public
      Workflows to calculate relative free energies using non-equilibrium switching for buried water molecules
      Python
      MIT License
      0400Updated Mar 22, 2026Mar 22, 2026
    • Lab website
      SCSS
      MIT License
      1400Updated Feb 28, 2026Feb 28, 2026
    • Jupyter notebooks for ligand optimization studies involving active learning
      Jupyter Notebook
      MIT License
      2710Updated Feb 24, 2026Feb 24, 2026
    • Input files used for simulations to test slow-rotations
      Shell
      0100Updated Jan 15, 2026Jan 15, 2026
    • Training

      Public
      Lab policies, training, style guides, etc.
      MIT License
      53501Updated Dec 9, 2025Dec 9, 2025
    • blues

      Public
      Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling
      Python
      MIT License
      1634156Updated Nov 12, 2025Nov 12, 2025
    • ssBind

      Public
      Python
      MIT License
      2000Updated Nov 10, 2025Nov 10, 2025
    • Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.
      Jupyter Notebook
      Creative Commons Attribution 4.0 International
      4416680Updated Mar 11, 2025Mar 11, 2025
    • Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
      Python
      MIT License
      82821Updated Dec 4, 2024Dec 4, 2024
    • Jupyter Notebook
      MIT License
      1300Updated Nov 18, 2024Nov 18, 2024
    • chemper

      Public
      Repository for Chemical Perception Sampling Tools
      Python
      MIT License
      1022161Updated Aug 13, 2024Aug 13, 2024
    • Jupyter Notebook
      MIT License
      2400Updated Jul 9, 2024Jul 9, 2024
    • An open tool implementing some recommended practices for analyzing alchemical free energy calculations
      Python
      MIT License
      62137243Updated May 24, 2024May 24, 2024
    • Scripts for local gromacs input file preparation
      0101Updated Apr 21, 2024Apr 21, 2024
    • T4_MSM

      Public
      Code and files for analyzing the discrete conformational states of T4 L99A
      Jupyter Notebook
      MIT License
      0100Updated Mar 8, 2024Mar 8, 2024
    • Computational enumeration of DNA-encoded libraries with various building block filtering and selection strategies
      Jupyter Notebook
      3500Updated Jan 16, 2024Jan 16, 2024
    • Code to analyze the data from DNA-encoded libraries (DELs)
      Jupyter Notebook
      MIT License
      11100Updated Jul 12, 2023Jul 12, 2023
    • HiMap

      Public
      High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP)
      Python
      MIT License
      21630Updated May 3, 2023May 3, 2023
    • Supporting information for paper on benchmarking enhanced sampling techniques for water sampling
      Python
      MIT License
      0100Updated Apr 5, 2023Apr 5, 2023
    • Scripts relating to setup of binding studies for the GROMACS simulation package
      MIT License
      0100Updated Nov 4, 2022Nov 4, 2022
    • Python
      MIT License
      0000Updated Sep 15, 2022Sep 15, 2022
    • Python
      0100Updated Sep 1, 2022Sep 1, 2022
    • Analysis scripts for the development of wiberg bond order interpolated parameters in the Open Force Field.
      Jupyter Notebook
      MIT License
      3204Updated Jun 16, 2022Jun 16, 2022
    • Python
      MIT License
      0000Updated May 2, 2022May 2, 2022
    • Supporting information for a paper benchmarking PME vs RF performance for relative free energies
      0100Updated May 2, 2022May 2, 2022
    • Lomap

      Public archive
      Alchemical mutation scoring map
      Python
      MIT License
      174100Updated Apr 7, 2022Apr 7, 2022
    • Experimental small molecule hydration free energy dataset
      Python
      Creative Commons Attribution 4.0 International
      83141Updated Mar 29, 2022Mar 29, 2022
    • Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
      TeX
      BSD 3-Clause "New" or "Revised" License
      1847232Updated Sep 29, 2021Sep 29, 2021
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