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    49 repositories

    • ALG_mannosyltransferase

      Public
      Scripts for molecular dynamics for ALG9 and analysis
      Jupyter Notebook
      •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • DASH-tree

      Public
      Partial Charge assignment for Molecular Dynamics
      Python
      •
      MIT License
      •7•23•0•2•Updated Dec 15, 2025Dec 15, 2025

    • TorsionDistributionFitting

      Public
      A tool for the automatic fitting of torsion motif angle distributions with Wrapped Mirrored Gaussians.
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Nov 19, 2025Nov 19, 2025

    • TorsionMotifTorsionAngleDistributions

      Public
      Unraveling Torsional Preferences: Comparative Analysis of Torsion Motif Torsion Angle Distributions Across Different Environments
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Nov 19, 2025Nov 19, 2025

    • lightweight-registration

      Public
      lwreg is a lightweight registration system for chemical registration and data storage.
      Jupyter Notebook
      •
      MIT License
      •17•81•7•0•Updated Nov 9, 2025Nov 9, 2025

    • conformational_domino

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 10, 2025Oct 10, 2025

    • cooperative-free-energy

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

    • QM-GNNIS

      Public
      Graph Neural Network Based Implicit QM Solvent
      Jupyter Notebook
      •
      MIT License
      •2•6•0•0•Updated Aug 28, 2025Aug 28, 2025

    • qmmm_reeds

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jul 10, 2025Jul 10, 2025

    • glauconic_acid

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

    • 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 states.
      Jupyter Notebook
      •
      MIT License
      •2•16•0•1•Updated Jul 3, 2025Jul 3, 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 binding free energies.
      pythonworkflowhpcdrug-designenhanced-samplingedsfree-energy-calculationsreplica-exchangegromos
      Python
      •
      MIT License
      •9•32•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

    • amp_qmmm

      Public
      Python
      •
      MIT License
      •2•2•0•0•Updated May 14, 2025May 14, 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-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
      •
      MIT No Attribution
      •6•50•4•0•Updated Apr 30, 2025Apr 30, 2025

    • gromosXX

      Public
      md++ code
      C++
      •
      GNU General Public License v2.0
      •6•1•0•0•Updated Mar 31, 2025Mar 31, 2025

    • gromosPlsPls

      Public
      C++
      •
      GNU General Public License v2.0
      •5•0•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•8•0•0•Updated Nov 8, 2024Nov 8, 2024

    • msms_wrapper

      Public
      Small python wrapper for the msms program
      Python
      •
      MIT License
      •1•5•1•0•Updated Oct 29, 2024Oct 29, 2024

    • cadd_exercises

      Public
      Exercises from TeachOpenCADD for the ETH Intro to CADD course
      Jupyter Notebook
      •0•3•0•0•Updated Oct 21, 2024Oct 21, 2024

    • reeds_protonation_tautomers

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

    • C-REMDforFRET

      Public
      Influence of the fluorophore mobility on distance measurements by gas phase FRET
      Jupyter Notebook
      •
      MIT No Attribution
      •0•0•0•0•Updated Jun 5, 2024Jun 5, 2024

    • mdfptools

      Public
      Jupyter Notebook
      •
      MIT License
      •2•7•3•0•Updated Jun 3, 2024Jun 3, 2024

    • Ensembler

      Public
      Ensembler is a python package that provides fast and easy access to 1D and 2D model system simulations. It can be used for method development or to deepen understanding of a broad spectrum of modeling methods, from basic sampling techniques to enhanced sampling and free energy calculations. It is easy to install, fast, increases shareability, co…
      visualizationpythonjupytersimulationteachingobject-orientedsymbolic-mathmethod-developmentpotential-functionstoy-models
      Python
      •
      MIT License
      •9•55•6•1•Updated May 3, 2024May 3, 2024

    • molecular_time_series

      Public
      Code and datasets from the publication https://doi.org/10.1186/s13321-023-00787-9
      Jupyter Notebook
      •
      MIT License
      •1•21•0•0•Updated Apr 21, 2024Apr 21, 2024

    • MD_and_NMR_Relaxometry

      Public
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Mar 13, 2024Mar 13, 2024

    • overlapping_assays

      Public
      Code and datasets from the manuscript "Comparing IC50 or Ki values from different sources is a source of significant noise".
      Jupyter Notebook
      •
      MIT License
      •9•42•2•0•Updated Jan 10, 2024Jan 10, 2024

    • reeds_applications

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 5, 2023Dec 5, 2023

    • ANA2B

      Public
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Nov 1, 2023Nov 1, 2023