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    27 repositories

    • ABFE_workflow

      Public
      This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.
      Python
      •
      GNU General Public License v3.0
      •20•61•11•0•Updated Dec 17, 2025Dec 17, 2025

    • AEV-PLIG-refined

      Public
      A refined version of the AEV-PLIG scoring function
      Python
      •
      Other
      •2•0•0•0•Updated Dec 3, 2025Dec 3, 2025

    • AEV-PLIG-data

      Public
      1•0•0•0•Updated Dec 3, 2025Dec 3, 2025

    • bee_alpha5

      Public
      Simulation data for "Characterization of a novel nicotinic acetylcholine receptor subtype preferentially sensitive to biogenic amines"
      Shell
      •2•0•0•0•Updated Nov 5, 2025Nov 5, 2025

    • spyrmsd

      Public
      📐 Symmetry-corrected RMSD in Python
      Python
      •
      MIT License
      •10•3•0•0•Updated May 7, 2025May 7, 2025

    • PoreAnalyser

      Public
      PoreAnalyser is package written by @DSeiferth that expands HOLE results to consider asymmetry and estimate conductance
      Python
      •
      GNU Lesser General Public License v2.1
      •2•1•0•0•Updated Feb 7, 2025Feb 7, 2025

    • AEV-PLIG

      Public
      Fork of the AEV-PLIG Repo
      Python
      •
      Other
      •16•3•0•0•Updated Dec 10, 2024Dec 10, 2024

    • PyCEC

      Public
      PyCEC
      Jupyter Notebook
      •
      Other
      •1•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • NoiseEstimator

      Public
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated May 30, 2024May 30, 2024

    • PyMEMENTO

      Public
      PyMEMENTO
      Python
      •
      GNU Lesser General Public License v3.0
      •4•1•0•0•Updated Apr 19, 2024Apr 19, 2024

    • aescore

      Public
      Learning Protein-Ligand Properties with Atomic Environment Vectors
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •14•10•0•0•Updated Apr 19, 2024Apr 19, 2024

    • WaterDock_pymol

      Public
      pymol implementation of WaterDock with Akshay Sridhar (@akshay-sridhar) and refactoring work by Patrick McCubbin (@mccubbinp)
      Python
      •
      GNU General Public License v3.0
      •7•11•0•0•Updated Mar 25, 2024Mar 25, 2024

    • WaterDock-2.0

      Public
      WaterDock-2.0 implementation with Akshay Sridhar
      Python
      •
      MIT License
      •8•21•0•0•Updated Nov 2, 2023Nov 2, 2023

    • Macroconf

      Public
      MacroConf Dataset & Workflows to Assess Cyclic Peptide Solution Structures
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •2•7•0•0•Updated Jun 21, 2023Jun 21, 2023

    • TB5-IntroductionToPython

      Public
      Notebook contents for the TB5 Introduction to Python course
      Jupyter Notebook
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•1•1•0•Updated Feb 17, 2023Feb 17, 2023

    • anion-polarization

      Public
      Effects of induced polarization on the nanoscale behaviour of anions in synthetic carriers
      Shell
      •1•0•0•0•Updated Feb 1, 2023Feb 1, 2023

    • OxCompBio

      Public
      Materials for the oxford computational biochemistry course including python
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •17•50•21•0•Updated Dec 13, 2022Dec 13, 2022

    • nav-alt-splice

      Public
      Code from Will Glass for Voltage-gated Sodium channel analysis
      Python
      •1•0•0•0•Updated Mar 21, 2022Mar 21, 2022

    • fragment-opt-abfe-benchmark

      Public
      Benchmark set for absolute binding free energy calculations of fragment optimisations
      Python
      •
      GNU General Public License v3.0
      •2•4•0•0•Updated Jan 28, 2022Jan 28, 2022

    • rocklinc

      Public
      A python module for performing Rocklin Correction.
      Python
      •
      MIT License
      •4•0•0•0•Updated Dec 11, 2021Dec 11, 2021

    • chap

      Public
      CHAP is a tool for the functional annotation of ion channel structures:
      C++
      •
      Other
      •10•0•0•0•Updated Dec 9, 2021Dec 9, 2021

    • alchemicalitp

      Public
      mirror of alchemicalitp from @xiki-tempula
      Python
      •
      MIT License
      •0•0•1•0•Updated Jan 5, 2021Jan 5, 2021

    • Bookshelf

      Public
      Bookshelf - a simple tool to help manage trajectory data.
      Python
      •
      GNU Lesser General Public License v2.1
      •0•0•0•0•Updated Jan 5, 2021Jan 5, 2021

    • OxCompBio-Datafiles

      Public
      Datafiles for the MD tutorial of the OxCompBio course (for ARCUS use only)
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Dec 15, 2020Dec 15, 2020

    • protein_orientation

      Public
      Mirror of Will Glass (github.com/WG150)'s code for protein orientation as recently published in Computational Investigation of Voltage-Gated Sodium Channel β3 S…
      Python
      •0•0•0•0•Updated May 6, 2020May 6, 2020

    • lintools

      Public
      Python script that creates 2D protein-ligand interaction images
      Python
      •
      GNU General Public License v3.0
      •13•2•5•2•Updated Jun 20, 2019Jun 20, 2019

    • lintools-laura-domicevica-mirror

      Public
      Mirror of the LINTools package with Laura Domicevica
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 20, 2016Jul 20, 2016