matsunagalab Goto Github PK

.github

benchmark_baumwelch

benchmark codes of Baum-Welch algorithm coparing MATLAB, Python, and Julia

capsid

Capsid tiling study

colabbtr

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

deeph3-distances-orientations

demo_ss_prediction

demonstration for predicting secondary structures

deprecated_afm

AFM image analysis using similar approaches proposed by BioEM

deprecated_web

mkdoc markdown for web https://www.bio.ics.saitama-u.ac.jp

differentiable

test-bed for differentiable parameter optimization of molecular systems

differentiable_btr

Jupyter notebooks for end-to-end differentiable blind tip reconstruction

docker-openmm

dockerfile for openmm

fepsuite

Software package for FEP

howto

hugo

hugo files

lecture_ml

Google colab notebooks used in a lecture on machine learning

lecture_ml_julia

Nextjournal notebooks for a lecture on machine learning written in Julia

lecture_ode

Lecuture notes on practical methods for ordinary differential equations

lecture_or

Google colab notebook for a lecture on Operations Research

matsunagalab.github.io

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

md_inputs

Place of learning OpenMM

mdtoolbox.jl

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

molly.jl

Molecular simulation in Julia

openmm-tutorials

Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM

paper_higashida2021

paper_mbar

Input files used in the paper on MBAR by Matsunaga et al.

paper_ogane2022

Files used in Ogane et al.

slide

test

tutorial_analyzingmddata

Google colab notebooks for typical MD trajectory analysis routines with Python

tutorial_hmm

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