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matsunagalab

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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. tutorial_hmm tutorial_hmm Public

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

    Jupyter Notebook 4 2

  3. lecture_ML lecture_ML Public

    Google colab notebooks used in a lecture on machine learning

    Jupyter Notebook 4

  4. docker-openmm docker-openmm Public

    dockerfile for openmm

    Shell 3 3

  5. ColabBTR ColabBTR Public

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

    Jupyter Notebook 3 3

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

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

    HTML 1

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