JackYang825

JackYang825's Stars

• qiangbo1222/Uni-RXN-official

  Language:Jupyter Notebook242

• OATML-Markslab/ProteinNPT

  Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"

  Language:Python919

• KULL-Centre/_2024_cagiada_stability

  Language:Jupyter Notebook576

• fhalab/MLDE

  A machine-learning package for navigating combinatorial protein fitness landscapes.

  Language:Python12326

• OATML-Markslab/ProteinGym

  Official repository for the ProteinGym benchmarks

  Language:HTML25330

• bzho3923/ProtLGN

  Language:Python268

• simonsnitz/plotting

  Language:Python1

• danny305/MutComputeX

  Language:Python207

• KaringX/karing

  Simple & Powerful proxy utility, Support routing rules for clash/sing-box

  Language:Dart3.8k332

• shap/shap

  A game theoretic approach to explain the output of any machine learning model.

  Language:Jupyter Notebook23.2k3.3k

• bayer-science-for-a-better-life/topefind-public

  Finding the pitfalls of deep learning predictors of interacting residues in antibodies 🦠

  Language:Python22

• jianqingzheng/XBCR-net

  [Cell Research] Deep learning-based rapid generation of broadly reactive antibodies against SARS-CoV-2 and its Omicron variant

  Language:Python312

• baker-laboratory/rf_diffusion_all_atom

  Public RFDiffusionAA repo

  Language:Python33856

• AbSciBio/unlocking-de-novo-antibody-design

  10616

• PKU-YuanGroup/ProLLaMA

  A Protein Large Language Model for Multi-Task Protein Language Processing

  Language:Python15318

• drorlab/atom3d

  ATOM3D: tasks on molecules in three dimensions

  Language:Python30435

• Xiaoxiao0606/BERT2DAb

  A pre-trained model for antibody squences

  Language:Python61

• togethercomputer/stripedhyena

  Repository for StripedHyena, a state-of-the-art beyond Transformer architecture

  Language:Python31826

• AWHKU/TOPVIP

  1

• tommyhuangthu/EvoEF2

  a fast and accurate physical energy function extended from EvoEF for protein sequence design

  Language:C++258

• pagnani/ArDCA.jl

  Autoregressive networks for protein

  Language:Jupyter Notebook369

• enai4bio/DeepAAI

  DeepAAI

  Language:Python303

• oxpig/CaLM

  Protein language model trained on coding DNA

  Language:Python4110

• evo-design/evo

  Biological foundation modeling from molecular to genome scale

  Language:Jupyter Notebook1.2k151

• LPDI-EPFL/masif_seed

  Masif seed paper repository

  Language:Jupyter Notebook14034

• gcorso/DiffDock

  Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

  Language:Python1.1k272

• zrqiao/NeuralPLexer

  NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

  Language:Jupyter Notebook27572

• bjornwallner/DockQ

  DockQ is a single continuous quality measure for Protein, Nucleic Acids and Small Molecule Docking Models

  Language:Python23653

• GeomMolDesign/HMR

  Code for "Learning Harmonic Molecular Representations on Riemannian Manifold", ICLR, 2023

  11

• westlake-repl/ProteinLM-TDG2-Mutation

  Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing

  Language:Jupyter Notebook131