ymatsunaga

ymatsunaga's Stars

• greener-group/rev-sim

  Reversible molecular simulation

  Language:Julia5

• RikenSugitaLab/MLMM-Potential

  Developing Machine Learning Potential for QM/MM

  Language:Fortran31

• SBQ-1999/CryFold

  From cryo-EM density map to atomic structure

  Language:Python232

• probabilists/lampe

  Likelihood-free AMortized Posterior Estimation with PyTorch

  Language:Python12112

• flatironinstitute/cryoSBI

  Language:Python9

• samuelmurail/SST2

  SST2 implementation in openmm

  Language:Jupyter Notebook3

• google-deepmind/alphafold3

  AlphaFold 3 inference pipeline.

  Language:Python5.7k669

• BILAB/psico

  PyMOL scripts

  Language:Python2

• rotskoff/shelfrich

  Monte Carlo simulations of bacterial microcompartment self-assembly

  Language:C++51

• arj7192/MasteringPyTorchV2

  Language:Jupyter Notebook9240

• chaidiscovery/chai-lab

  Chai-1, SOTA model for biomolecular structure prediction

  Language:Python1.5k187

• ImagineAILab/ai-by-hand-excel

  2.3k332

• Das0Mann/MolSpin

  Software package for spin dynamics

  Language:C++71

• fwilliams/scalable-pytorch-sinkhorn

  Language:Python1417

• whitead/symd

  N-Dimensional MD engine with symmetry group constraints written in C

  Language:Jupyter Notebook436

• Olemi-llm-apprentice/generate-project-summary

  プロジェクトのファイル階層や記述内容を一つのテキストファイルにまとめる

  Language:Python11111

• bjing2016/mdgen

  Generative modeling of molecular dynamics trajectories

  Language:Python12514

• iamhyc/Overleaf-Workshop

  Open Overleaf/ShareLaTex projects in vscode, with full collaboration support.

  Language:TypeScript62514

• yamadashy/repomix

  📦 Repomix (formerly Repopack) is a powerful tool that packs your entire repository into a single, AI-friendly file. Perfect for when you need to feed your codebase to Large Language Models (LLMs) or other AI tools like Claude, ChatGPT, and Gemini.

  Language:TypeScript5.6k275

• hanyoseob/pytorch-noise2void

  Noise2Void - Learning Denoising from Single Noisy Images

  Language:Python11614

• chand1012/git2gpt

  Convert a Git repo into a ChatGPT prompt!

  Language:Go13615

• Ligo-Biosciences/AlphaFold3

  Open source implementation of AlphaFold3

  Language:Python94283

• ghorbanimahdi73/GraphVampNet

  Language:Jupyter Notebook155

• universvm/how_to_create_a_protein

  A short course on proteins and protein design aimed at early career students

  1446

• yaledeus/FBM

  Force-Guided Bridge Matching for Full-Atom Time-Coarsened Dynamics of Peptides

  Language:Python81

• xuhuihuang/graphvampnets

  GraphVAMPnets combines graph neural networks with variational approach for Markovian process (VAMP) theory to identify the slow collective variables of the self-assembly processes.

  Language:Python115

• westlake-repl/ProTrek

  ProTrek: Navigating the Protein Universe through Tri-Modal Contrastive Learning

  Language:Python688

• karpathy/nn-zero-to-hero

  Neural Networks: Zero to Hero

  Language:Jupyter Notebook12.4k1.6k

• arcee-ai/mergekit

  Tools for merging pretrained large language models.

  Language:Python5k458

• nianticlabs/manydepth

  [CVPR 2021] Self-supervised depth estimation from short sequences

  Language:Python62985