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@moldyn

Biomolecular Dynamics

Group of Prof. Dr. G. Stock, University of Freiburg
README.md

Welcome at MolDyn Freiburg 👋

Understanding elementary life processes from first principles.

Working in theoretical biological physics in close collaboration with experimental groups, we are concerned with the theory and simulation of elementary biomolecular processes. In particular, we strive to design new multiscale simulation methods and develop novel strategies to reduce the complexity of nonequilibrium phenomena.

Checkout our website for a list of all publications 📚, fields of research :atom:🧬🔬, or to get in contact with us.

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  1. MoSAIC MoSAIC Public

    Correlation-based feature selection of Molecular Dynamics simulations

    Python 29 3

  2. Clustering Clustering Public

    Robust and stable clustering of molecular dynamics simulation trajectories.

    C++ 19 6

  3. dcTMD dcTMD Public

    Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.

    Python 17 1

  4. msmhelper msmhelper Public

    Helper function for Markov State Models

    Python 11 3

  5. FastPCA FastPCA Public

    Forked from lettis/FastPCA

    Fast, parallelized implementation of Principal Component Analysis with constant memory consumption for large data sets.

    C 12 2

  6. MSMPathfinder MSMPathfinder Public

    Finding pathways from an Markov State Model

    C++ 9 3

Repositories

Showing 10 of 23 repositories
  • GP-TEMPEST Public

    Gaussian Process Temporal Embedding for Protein Simulations and Transitions

    moldyn/GP-TEMPEST’s past year of commit activity
    Python 2 0 0 0 Updated Mar 20, 2026
  • dcTMD Public

    Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.

    moldyn/dcTMD’s past year of commit activity
    Python 17 MIT 1 0 0 Updated Feb 27, 2026
  • MPP Public

    Implementation of the Most Probable Path (MPP) algorithm for the coarse-graining of state trajectories, e.g. as obtained from Molecular Dynamics simulations.

    moldyn/MPP’s past year of commit activity
    Python 1 MIT 0 0 0 Updated Feb 14, 2026
  • NorMI Public

    Generalized Kraskov Estimator for Normalized Mutual Information

    moldyn/NorMI’s past year of commit activity
    Python 23 MIT 2 3 0 Updated Dec 16, 2025
  • MoSAIC Public

    Correlation-based feature selection of Molecular Dynamics simulations

    moldyn/MoSAIC’s past year of commit activity
    Python 29 MIT 3 0 0 Updated Nov 25, 2025
  • tutorial_dcTMD Public Forked from floWneffetS/tutorial_dcTMD

    Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.

    moldyn/tutorial_dcTMD’s past year of commit activity
    Python 2 GPL-3.0 4 0 0 Updated Jul 15, 2024
  • msmhelper Public

    Helper function for Markov State Models

    moldyn/msmhelper’s past year of commit activity
    Python 11 BSD-3-Clause 3 0 1 Updated Jun 25, 2024
  • HP35 Public

    Selecting Features for Markov Modeling: A Case Study on HP35

    moldyn/HP35’s past year of commit activity
    HiveQL 12 BSD-3-Clause 2 2 0 Updated May 25, 2023
  • HP35-DESRES Public

    DESRES trajectory of wild type HP-35 at 360K

    moldyn/HP35-DESRES’s past year of commit activity
    7 0 0 0 Updated May 16, 2023
  • 2Dmodel_path_analysis Public Forked from floWneffetS/2Dmodel_path_analysis

    Jupyter notebook with 2D test potential energy landscape for performing model biased simulations combined with pathway analysis.

    moldyn/2Dmodel_path_analysis’s past year of commit activity
    Jupyter Notebook 1 1 0 0 Updated Jan 16, 2023
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