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    38 repositories

    • TorsionAngularBinStrings

      Public
      (T)orsion (A)ngular (B)in (S)trings: Quantifying flexibility by introducing a discrete vector representation of a conformer's dihedral angles to allow for counting of states.
      Jupyter Notebook
      •
      MIT License
      •1•7•0•0•Updated Oct 15, 2024Oct 15, 2024

    • cadd_exercises

      Public
      Exercises from TeachOpenCADD for the ETH Intro to CADD course
      Jupyter Notebook
      •0•3•0•0•Updated Oct 13, 2024Oct 13, 2024

    • glauconic_acid

      Public
      Python
      •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • lightweight-registration

      Public
      Jupyter Notebook
      •
      MIT License
      •14•61•7•2•Updated Sep 17, 2024Sep 17, 2024

    • DASH-tree

      Public
      Partial Charge assignment for Molecular Dynamics
      Python
      •
      MIT License
      •6•16•0•0•Updated Aug 19, 2024Aug 19, 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•2•0•0•Updated Jun 28, 2024Jun 28, 2024

    • GNNImplicitSolvent

      Public
      Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations
      Jupyter Notebook
      •
      MIT No Attribution
      •2•17•0•0•Updated Jun 19, 2024Jun 19, 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•4•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…
      visualizationjupyterteachingobject-orientedsymbolic-mathmethod-developmentpotential-functionstoy-modelspythonsimulation
      Python
      •
      MIT License
      •9•50•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•19•0•0•Updated Apr 21, 2024Apr 21, 2024

    • msms_wrapper

      Public
      Small python wrapper for the msms program
      GLSL
      •
      MIT License
      •1•4•1•0•Updated Apr 10, 2024Apr 10, 2024

    • MD_and_NMR_Relaxometry

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

    • 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
      •8•29•3•0•Updated Feb 18, 2024Feb 18, 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
      •4•29•1•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•2•0•0•Updated Nov 1, 2023Nov 1, 2023

    • PyGromosTools

      Public
      This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.
      pythonapiwrappersimulationmolecular-dynamicscomputational-chemistryrdkitmdenergy-minimizationopenforcefield
      Python
      •
      MIT License
      •14•16•9•4•Updated Oct 17, 2023Oct 17, 2023

    • teachopencadd

      Public
      TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •202•2•0•0•Updated Aug 30, 2023Aug 30, 2023

    • irsa

      Public
      Python
      •
      MIT License
      •2•9•2•0•Updated Aug 7, 2023Aug 7, 2023

    • EnergyBasedClustering

      Public
      Implementation of Energy Based Clustering
      Jupyter Notebook
      •
      MIT License
      •0•11•0•0•Updated Jul 20, 2023Jul 20, 2023

    • HybridTopologyViewer

      Public
      Python
      •0•1•0•0•Updated Apr 13, 2023Apr 13, 2023

    • decapeptides-membrane

      Public
      Contains the necessary material to reproduce the content of the paper: Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Feb 9, 2023Feb 9, 2023

    • restraintmaker

      Public
      Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation technique with coordinate-based particles). It can be used on a script layer or as an interactive plugin for PyMol. Features are different selection modes and Optimizers to distribute restraints.
      interactivepymol-pluginpython3md-simulationsfree-energy-calculationsrestraintstopology-buildingsystem-generationpython
      Python
      •
      MIT License
      •4•17•0•0•Updated Oct 27, 2022Oct 27, 2022

    • gregs-test-project

      Public
      0•0•0•0•Updated Oct 10, 2022Oct 10, 2022

    • GHOST

      Public
      Jupyter Notebook
      •
      MIT License
      •13•48•1•0•Updated Aug 1, 2022Aug 1, 2022

    • GNNParametrizedFF

      Public
      Repository for the models used in the publication 'Regularized by Physics: Graph Neural Network Parametrized Potentials for the Description of Intermolecular Interactions'
      Python
      •
      MIT License
      •1•8•1•0•Updated Jun 2, 2022Jun 2, 2022

    • EquivariantMultipoleGNN

      Public
      Equivariant GNN for the prediction of atomic multipoles up to quadrupoles.
      Jupyter Notebook
      •
      MIT License
      •7•28•1•0•Updated May 12, 2022May 12, 2022

    • customETKDG

      Public
      Python
      •2•12•1•1•Updated Mar 9, 2022Mar 9, 2022