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Repositories of Matsunaga Lab

  • protein G Correcting folding pathway of Protein G by integrative modeling with Markov state model
  • myosin V Hidden Markov Modeling of Myosin V Walking on Actin Filament using High-Speed Atomic Force Microscopy Data
  • capsid Explicit description of viral capsid subunit shapes by expanding dihedrons
  • differentiable_BTR End-to-end differentiable blind tip reconstruction for noisy atomic force microscopy images
  • paper_mbar Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation
  • paper_ogane2022 Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images
  • paper_higashida2021 Enhanced Conformational Sampling of Nanobody CDR H3 Loop by Generalized Replica-Exchange with Solute Tempering

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  1. MDToolbox.jl MDToolbox.jl Public

    MDToolbox.jl: A Julia package for molecular dynamics trajectories analysis and modeling of biomolecules

    Julia 21 5

  2. lecture_ML lecture_ML Public

    Google colab notebooks used in a lecture on machine learning

    Jupyter Notebook 4

  3. docker-openmm docker-openmm Public

    dockerfile for openmm

    Shell 3 3

  4. tutorial_hmm tutorial_hmm Public

    Hands-on tutorials for Markov state modeling of MD and EXP data

    Jupyter Notebook 3 2

  5. ColabBTR ColabBTR Public

    End-to-end differentiable blind tip reconstruction on Colab implemented with PyTorch

    Jupyter Notebook 2 2

  6. matsunagalab.github.io matsunagalab.github.io Public

    for deploy with GitHub pages https://matsunagalab.github.io

    HTML 1

Repositories

Showing 10 of 33 repositories
  • genesis Public Forked from genesis-release-r-ccs/genesis

    Source, test set, and document for Molecular Dynamics software, GENESIS.

    matsunagalab/genesis’s past year of commit activity
    Fortran 0 LGPL-3.0 9 0 0 Updated Dec 22, 2024
  • capsid_view Public
    matsunagalab/capsid_view’s past year of commit activity
    HTML 0 MIT 1 1 0 Updated Dec 17, 2024
  • howto Public
    matsunagalab/howto’s past year of commit activity
    0 MIT 0 0 0 Updated Dec 12, 2024
  • ColabBTR Public

    End-to-end differentiable blind tip reconstruction on Colab implemented with PyTorch

    matsunagalab/ColabBTR’s past year of commit activity
    Jupyter Notebook 2 MIT 2 0 0 Updated Dec 5, 2024
  • matsunagalab.github.io Public

    for deploy with GitHub pages https://matsunagalab.github.io

    matsunagalab/matsunagalab.github.io’s past year of commit activity
    HTML 1 0 0 0 Updated Dec 4, 2024
  • md_inputs Public

    Place of learning OpenMM

    matsunagalab/md_inputs’s past year of commit activity
    Rich Text Format 0 MIT 0 0 0 Updated Nov 23, 2024
  • hugo Public

    hugo files

    matsunagalab/hugo’s past year of commit activity
    0 0 0 0 Updated Nov 19, 2024
  • lecture_OR Public

    Google colab notebook for a lecture on Operations Research

    matsunagalab/lecture_OR’s past year of commit activity
    Jupyter Notebook 0 MIT 1 0 0 Updated Nov 19, 2024
  • differentiable Public

    test-bed for differentiable parameter optimization of molecular systems

    matsunagalab/differentiable’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Nov 12, 2024
  • .github Public
    matsunagalab/.github’s past year of commit activity
    0 0 0 0 Updated Nov 12, 2024

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