matsunagalab

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33 repositories

genesis
Public
Source, test set, and document for Molecular Dynamics software, GENESIS.
Fortran
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GNU Lesser General Public License v3.0
•9•0•0•0•Updated Dec 22, 2024Dec 22, 2024
capsid_view
Public
HTML
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MIT License
•1•0•1•0•Updated Dec 17, 2024Dec 17, 2024
howto
Public
students research thesis
MIT License
•0•0•0•0•Updated Dec 12, 2024Dec 12, 2024
ColabBTR
Public
End-to-end differentiable blind tip reconstruction on Colab implemented with PyTorch
afm differentiable-programming atomic-force-microscopy blind-tip-reconstruction
Jupyter Notebook
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MIT License
•2•2•0•0•Updated Dec 5, 2024Dec 5, 2024
matsunagalab.github.io
Public
for deploy with GitHub pages https://matsunagalab.github.io
web lab
HTML
•0•1•0•0•Updated Dec 4, 2024Dec 4, 2024
md_inputs
Public
Place of learning OpenMM
molecular-dynamics openmm
Rich Text Format
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MIT License
•0•0•0•0•Updated Nov 23, 2024Nov 23, 2024
hugo
Public
hugo files
0•0•0•0•Updated Nov 19, 2024Nov 19, 2024
lecture_OR
Public
Google colab notebook for a lecture on Operations Research
coin operations-research pulp
Jupyter Notebook
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MIT License
•1•0•0•0•Updated Nov 19, 2024Nov 19, 2024
differentiable
Public
test-bed for differentiable parameter optimization of molecular systems
molecular-dynamics docking differentiable-programming
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Nov 12, 2024Nov 12, 2024
.github
Public
0•0•0•0•Updated Nov 12, 2024Nov 12, 2024
capsid
Public
Capsid tiling study
virus tiling capsid docking
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Oct 19, 2024Oct 19, 2024
tutorial_analyzingMDdata
Public
Google colab notebooks for typical MD trajectory analysis routines with Python
tutorial scikit-learn molecular-dynamics mdtraj
Jupyter Notebook
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MIT License
•0•1•0•0•Updated Sep 27, 2024Sep 27, 2024
MDToolbox.jl
Public
MDToolbox.jl: A Julia package for molecular dynamics trajectories analysis and modeling of biomolecules
molecular-dynamics biomolecule differentiable-programming julia
Julia
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Other
•5•21•0•0•Updated Sep 12, 2024Sep 12, 2024
differentiable_BTR
Public
Jupyter notebooks for end-to-end differentiable blind tip reconstruction
afm differentiable-programming hs-afm julia
Jupyter Notebook
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MIT License
•3•0•0•0•Updated Aug 31, 2024Aug 31, 2024
tutorial_viz
Public
MIT License
•0•0•0•0•Updated Jul 17, 2024Jul 17, 2024
lecture_ML
Public
Google colab notebooks used in a lecture on machine learning
scikit-learn torch pymc notebooks lecture
Jupyter Notebook
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GNU General Public License v3.0
•0•4•0•0•Updated Jul 15, 2024Jul 15, 2024
test
Public
AppleScript
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MIT License
•1•0•0•0•Updated Jul 1, 2024Jul 1, 2024
slide
Public
presentation powerpoint
MIT License
•0•0•0•0•Updated May 16, 2024May 16, 2024
Molly.jl
Public
Molecular simulation in Julia
Julia
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Other
•55•0•0•0•Updated Sep 8, 2023Sep 8, 2023
paper_higashida2021
Public
molecular-dynamics antibody replica-exchange nanobody vhh
Rich Text Format
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BSD 3-Clause "New" or "Revised" License
•1•1•0•0•Updated Jul 16, 2023Jul 16, 2023
lecture_ML_julia
Public
Nextjournal notebooks for a lecture on machine learning written in Julia
julia julia-language lecture
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Jun 25, 2023Jun 25, 2023
fepsuite
Public
Software package for FEP
Python
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GNU General Public License v3.0
•3•0•0•0•Updated May 1, 2023May 1, 2023
paper_ogane2022
Public
Files used in Ogane et al.
hmm afm julia hidden-markov-model hs-afm
Jupyter Notebook
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GNU General Public License v3.0
•0•0•0•0•Updated Nov 24, 2022Nov 24, 2022
paper_mbar
Public
Input files used in the paper on MBAR by Matsunaga et al.
molecular-dynamics multistate-bennett-acceptance-ratio
Rich Text Format
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GNU General Public License v3.0
•1•0•0•0•Updated Oct 18, 2022Oct 18, 2022
tutorial_hmm
Public
Hands-on tutorials for Markov state modeling of MD and EXP data
hidden-markov-model markov-state-model
Jupyter Notebook
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MIT License
•2•3•0•0•Updated Mar 9, 2021Mar 9, 2021
deepH3-distances-orientations
Public
Python
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Other
•9•0•0•0•Updated Nov 19, 2020Nov 19, 2020
demo_ss_prediction
Public
demonstration for predicting secondary structures
support-vector-machine secondary-structure
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jun 19, 2020Jun 19, 2020
docker-openmm
Public
dockerfile for openmm
docker openmm
Shell
•3•3•0•0•Updated May 27, 2020May 27, 2020
openmm-tutorials
Public
Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM
Rich Text Format
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MIT License
•18•0•0•0•Updated May 20, 2020May 20, 2020
deprecated_afm
Public
AFM image analysis using similar approaches proposed by BioEM
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Apr 27, 2020Apr 27, 2020