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    • Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations
      Jupyter Notebook
      MIT No Attribution
      11900Updated Dec 12, 2024Dec 12, 2024
    • amp_qmmm

      Public
      Python
      MIT License
      0000Updated Dec 2, 2024Dec 2, 2024
    • C++
      GNU General Public License v2.0
      3000Updated Nov 25, 2024Nov 25, 2024
    • gromosXX

      Public
      md++ code
      C++
      GNU General Public License v2.0
      6000Updated Nov 25, 2024Nov 25, 2024
    • Code and data for the paper "Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents"
      Jupyter Notebook
      0200Updated Nov 8, 2024Nov 8, 2024
    • Small python wrapper for the msms program
      Python
      MIT License
      1410Updated Oct 29, 2024Oct 29, 2024
    • Jupyter Notebook
      MIT License
      146572Updated Oct 29, 2024Oct 29, 2024
    • Exercises from TeachOpenCADD for the ETH Intro to CADD course
      Jupyter Notebook
      0300Updated Oct 21, 2024Oct 21, 2024
    • (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
      11000Updated Oct 15, 2024Oct 15, 2024
    • Python
      0000Updated Oct 11, 2024Oct 11, 2024
    • DASH-tree

      Public
      Partial Charge assignment for Molecular Dynamics
      Python
      MIT License
      61700Updated Aug 19, 2024Aug 19, 2024
    • Jupyter Notebook
      0000Updated Jun 7, 2024Jun 7, 2024
    • Influence of the fluorophore mobility on distance measurements by gas phase FRET
      Jupyter Notebook
      MIT No Attribution
      0000Updated Jun 5, 2024Jun 5, 2024
    • mdfptools

      Public
      Jupyter Notebook
      MIT License
      2740Updated 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…
      Python
      MIT License
      85161Updated May 3, 2024May 3, 2024
    • Code and datasets from the publication https://doi.org/10.1186/s13321-023-00787-9
      Jupyter Notebook
      MIT License
      11900Updated Apr 21, 2024Apr 21, 2024
    • Jupyter Notebook
      MIT License
      1200Updated 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.
      Python
      MIT License
      83030Updated Feb 18, 2024Feb 18, 2024
    • Code and datasets from the manuscript "Comparing IC50 or Ki values from different sources is a source of significant noise".
      Jupyter Notebook
      MIT License
      53210Updated Jan 10, 2024Jan 10, 2024
    • Jupyter Notebook
      0000Updated Dec 5, 2023Dec 5, 2023
    • ANA2B

      Public
      Jupyter Notebook
      MIT License
      0300Updated Nov 1, 2023Nov 1, 2023
    • 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.
      Python
      MIT License
      141694Updated Oct 17, 2023Oct 17, 2023
    • TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
      Jupyter Notebook
      Creative Commons Attribution 4.0 International
      209200Updated Aug 30, 2023Aug 30, 2023
    • irsa

      Public
      Python
      MIT License
      2920Updated Aug 7, 2023Aug 7, 2023
    • Implementation of Energy Based Clustering
      Jupyter Notebook
      MIT License
      01100Updated Jul 20, 2023Jul 20, 2023
    • Python
      0100Updated Apr 13, 2023Apr 13, 2023
    • 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
      0200Updated Feb 9, 2023Feb 9, 2023
    • 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.
      Python
      MIT License
      41700Updated Oct 27, 2022Oct 27, 2022
    • 0000Updated Oct 10, 2022Oct 10, 2022
    • GHOST

      Public
      Jupyter Notebook
      MIT License
      134810Updated Aug 1, 2022Aug 1, 2022