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    57 repositories

    • ALG8-glucosyltransferase

      Public
      Analysis Code for AMBER trajectory on ALG8
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 9, 2026Oct 9, 2026

    • TorsionAngularBinStrings

      Public
      Torsion Angular Bin Strings: Quantifying flexibility by introducing a discrete vector representation of a conformer's dihedral angles to allow for counting of s…
      Jupyter Notebook
      •
      MIT License
      •3•18•0•0•Updated Oct 8, 2026Oct 8, 2026

    • lightweight-registration

      Public
      lwreg is a lightweight registration system for chemical registration and data storage.
      Jupyter Notebook
      •
      MIT License
      •20•93•7•1•Updated Oct 5, 2026Oct 5, 2026

    • DASH-tree

      Public
      Partial Charge assignment for Molecular Dynamics
      Python
      •
      MIT License
      •6•24•0•2•Updated Aug 11, 2026Aug 11, 2026

    • gromosXX

      Public
      md++ code
      C++
      •
      GNU General Public License v2.0
      •8•2•0•0•Updated Jul 27, 2026Jul 27, 2026

    • geometrical_EDS

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 25, 2026Jul 25, 2026

    • SmoothTransformationWithEDS

      Public
      Code to run and analyze the data for the article "Smoother Alchemical Transformations via Enveloping Distribution Sampling for Free-Energy Estimation"
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 22, 2026Jul 22, 2026

    • QM-GNNIS

      Public
      Graph Neural Network Based Implicit QM Solvent
      Jupyter Notebook
      •
      MIT License
      •3•8•0•0•Updated Jul 18, 2026Jul 18, 2026

    • amp_qmmm

      Public
      Python
      •
      MIT License
      •2•7•0•0•Updated Jul 17, 2026Jul 17, 2026

    • amp_bms

      Public
      Python
      •
      MIT License
      •8•50•2•0•Updated Jul 17, 2026Jul 17, 2026

    • ChEMBL_MTL

      Public
      Evaluation of data curation strategies for bioactivity prediction using ChEMBL data
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Jun 24, 2026Jun 24, 2026

    • MAPRE1-FKBP12-Molecular-Glue

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 14, 2026Jun 14, 2026

    • ALG_mannosyltransferase

      Public
      Scripts for molecular dynamics for ALG9 and analysis
      Jupyter Notebook
      •1•0•0•0•Updated May 19, 2026May 19, 2026

    • rest2_ampmm

      Public
      Python
      •
      MIT License
      •1•7•0•0•Updated Apr 9, 2026Apr 9, 2026

    • conformational_domino

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • molecular_balances

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 13, 2026Jan 13, 2026

    • TorsionMotifTorsionAngleDistributions

      Public
      Unraveling Torsional Preferences: Comparative Analysis of Torsion Motif Torsion Angle Distributions Across Different Environments
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jan 7, 2026Jan 7, 2026

    • TorsionDistributionFitting

      Public
      A tool for the automatic fitting of torsion motif angle distributions with Wrapped Mirrored Gaussians.
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Nov 19, 2025Nov 19, 2025

    • cooperative-free-energy

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Sep 22, 2025Sep 22, 2025

    • qmmm_reeds

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Jul 10, 2025Jul 10, 2025

    • glauconic_acid

      Public
      Python
      •0•0•0•0•Updated Jul 9, 2025Jul 9, 2025

    • reeds

      Public
      This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand b…
      pythonworkflowhpc
      pythonworkflowhpcdrug-designenhanced-samplingedsfree-energy-calculationsreplica-exchangegromos
      Python
      •
      MIT License
      •9•34•2•2•Updated Jun 3, 2025Jun 3, 2025

    • mutanobactin-d-computational-repo

      Public
      Mutanobactin D - Computational Repo
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 26, 2025May 26, 2025

    • Physical_Chemistry_Practicum-Molecular_Dynamics_Simulations

      Public
      This repository is the used for teaching the Physical Chemistry Practicum about Molecular Dynamics (MD) simulations for pharmacy and biology students at ETHZ
      analysisbiologymolecular-dynamics
      analysisbiologymolecular-dynamicsteachingphysical-chemistrybachelormdpharmacyethz
      Jupyter Notebook
      •0•12•0•0•Updated May 7, 2025May 7, 2025

    • GNNImplicitSolvent

      Public
      Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations
      Jupyter Notebook
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      MIT No Attribution
      •9•57•5•0•Updated Apr 30, 2025Apr 30, 2025

    • gromosPlsPls

      Public
      C++
      •
      GNU General Public License v2.0
      •6•1•0•0•Updated Nov 25, 2024Nov 25, 2024

    • macrocycle-ff-validation

      Public
      Code and data for the paper "Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents"
      Jupyter Notebook
      •0•9•0•0•Updated Nov 8, 2024Nov 8, 2024

    • msms_wrapper

      Public
      Small python wrapper for the msms program
      Python
      •
      MIT License
      •1•6•1•0•Updated Oct 29, 2024Oct 29, 2024

    • cadd_exercises

      Public
      Exercises from TeachOpenCADD for the ETH Intro to CADD course
      Jupyter Notebook
      •0•4•0•0•Updated Oct 21, 2024Oct 21, 2024

    • reeds_protonation_tautomers

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jun 7, 2024Jun 7, 2024
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