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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 25 2

  2. Clustering Clustering Public

    Robust and stable clustering of molecular dynamics simulation trajectories.

    C++ 17 6

  3. dcTMD dcTMD Public

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

    Python 14

  4. msmhelper msmhelper Public

    Helper function for Markov State Models

    Python 8 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 9 2

  6. MSMPathfinder MSMPathfinder Public

    Finding pathways from an Markov State Model

    C++ 9 3

Repositories

Showing 10 of 21 repositories
  • NorMI Public

    Generalized Kraskov Estimator for Normalized Mutual Information

    moldyn/NorMI’s past year of commit activity
    Python 10 MIT 1 3 0 Updated Nov 21, 2024
  • MoSAIC Public

    Correlation-based feature selection of Molecular Dynamics simulations

    moldyn/MoSAIC’s past year of commit activity
    Python 25 MIT 2 2 1 Updated Nov 19, 2024
  • dcTMD Public

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

    moldyn/dcTMD’s past year of commit activity
    Python 14 MIT 0 1 2 Updated Jul 17, 2024
  • 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 8 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 8 BSD-3-Clause 1 1 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
    5 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
  • Clustering Public

    Robust and stable clustering of molecular dynamics simulation trajectories.

    moldyn/Clustering’s past year of commit activity
    C++ 17 BSD-2-Clause 6 1 0 Updated Sep 2, 2022
  • HP35-Benchmark Public

    Benchmarking dimensionality reduction methods and clustering on HP35-DESRES

    moldyn/HP35-Benchmark’s past year of commit activity
    Shell 1 BSD-3-Clause 0 0 0 Updated Aug 5, 2022
View all repositories

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