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    56 repositories

    • SeparatedTopologies

      Public
      Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
      Python
      •
      MIT License
      •8•22•0•2•Updated Nov 19, 2024Nov 19, 2024

    • ConformerDependentCharges

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

    • slow-rotations

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated Oct 10, 2024Oct 10, 2024

    • chemper

      Public
      Repository for Chemical Perception Sampling Tools
      Python
      •
      MIT License
      •10•19•16•1•Updated Aug 13, 2024Aug 13, 2024

    • qm-theory-benchmark

      Public
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Jul 9, 2024Jul 9, 2024

    • mobleylab.org

      Public
      Lab website
      SCSS
      •
      MIT License
      •1•4•0•0•Updated Jul 8, 2024Jul 8, 2024

    • alchemical-analysis

      Public
      An open tool implementing some recommended practices for analyzing alchemical free energy calculations
      Python
      •
      MIT License
      •60•120•24•4•Updated May 24, 2024May 24, 2024

    • gmx_fileprep

      Public
      Scripts for local gromacs input file preparation
      0•1•0•1•Updated Apr 21, 2024Apr 21, 2024

    • Training

      Public
      Lab policies, training, style guides, etc.
      MIT License
      •5•35•0•1•Updated Apr 1, 2024Apr 1, 2024

    • T4_MSM

      Public
      Code and files for analyzing the discrete conformational states of T4 L99A
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 8, 2024Mar 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.
      pythonmonte-carlomolecular-dynamicssolubilitymolecular-dynamics-simulationdrug-discoverydockingligand-screeningteaching-materialseducational-software
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •44•145•8•0•Updated Feb 28, 2024Feb 28, 2024

    • DEL_BB_design

      Public
      Computational enumeration of DNA-encoded libraries with various building block filtering and selection strategies
      Jupyter Notebook
      •2•3•0•0•Updated Jan 16, 2024Jan 16, 2024

    • DEL_analysis

      Public
      Code to analyze the data from DNA-encoded libraries (DELs)
      Jupyter Notebook
      •
      MIT License
      •1•8•0•0•Updated Jul 12, 2023Jul 12, 2023

    • HiMap

      Public
      High Information Mapper (HiMap), successor of the Lead Optimization Mapper (LOMAP)
      chemistrycheminformaticsalchemical-free-energy-calculationsgraph-optimization
      Python
      •
      MIT License
      •2•16•2•0•Updated May 3, 2023May 3, 2023

    • water_benchmark_paper

      Public
      Supporting information for paper on benchmarking enhanced sampling techniques for water sampling
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 5, 2023Apr 5, 2023

    • waterNES

      Public
      Workflows to calculate relative free energies using non-equilibrium switching for buried water molecules
      Python
      •
      MIT License
      •0•3•0•0•Updated Nov 18, 2022Nov 18, 2022

    • gromacs-binding-scripts

      Public
      Scripts relating to setup of binding studies for the GROMACS simulation package
      MIT License
      •0•1•0•0•Updated Nov 4, 2022Nov 4, 2022

    • FreeSolv

      Public
      Experimental and calculated small molecule hydration free energies
      solvationpythondatabasehydrationexperimental-datafree-energiescalculated-valuesexperimental-values
      Python
      •53•107•15•0•Updated Oct 14, 2022Oct 14, 2022

    • binding_dG_water

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 15, 2022Sep 15, 2022

    • fitting-exp

      Public
      Python
      •0•1•0•0•Updated Sep 1, 2022Sep 1, 2022

    • blues

      Public
      Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling
      Python
      •
      MIT License
      •16•33•14•7•Updated Jul 11, 2022Jul 11, 2022

    • wbointerpolation

      Public
      Analysis scripts for the development of wiberg bond order interpolated parameters in the Open Force Field.
      Jupyter Notebook
      •
      MIT License
      •3•2•0•4•Updated Jun 16, 2022Jun 16, 2022

    • GCNCMC_GCMC

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 2, 2022May 2, 2022

    • PME-RF-benchmark

      Public
      Supporting information for a paper benchmarking PME vs RF performance for relative free energies
      0•1•0•0•Updated May 2, 2022May 2, 2022

    • Lomap

      Public archive
      Alchemical mutation scoring map
      Python
      •
      MIT License
      •17•37•0•0•Updated Apr 7, 2022Apr 7, 2022

    • GuthrieSolv

      Public
      Experimental small molecule hydration free energy dataset
      databasehydrationsolvationwaterexperimental-datafree-energiesexperimental-values
      Python
      •
      Creative Commons Attribution 4.0 International
      •8•30•4•1•Updated Mar 29, 2022Mar 29, 2022

    • benchmarksets

      Public
      Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
      TeX
      •
      BSD 3-Clause "New" or "Revised" License
      •16•42•23•2•Updated Sep 29, 2021Sep 29, 2021

    • sampl7-physical-property-challenge-manuscript

      Public
      Provided are figures, tables, and supplementary documents for the "Evaluation of logP, pKa, and logD predictions from the SAMPL7 blind challenge" paper.
      0•0•0•0•Updated May 5, 2021May 5, 2021

    • benchmarkff

      Public
      Compare optimized geometries and energies from various force fields with respect to a QM reference.
      Python
      •
      MIT License
      •8•13•7•2•Updated Apr 19, 2021Apr 19, 2021

    • openff-spellbook

      Public
      Handy functionality for working with OpenFF data
      Python
      •
      MIT License
      •2•3•1•0•Updated Apr 10, 2021Apr 10, 2021