JackYang825

JackYang825's Stars

• dptech-corp/Uni-Core

  an efficient distributed PyTorch framework

  Language:Python12533

• iambic-therapeutics/np-bench

  A benchmark for 3D biomolecular structure prediction models

  Language:Python483

• GENTEL-lab/EnzymeCAGE

  Language:Python254

• DeepGraphLearning/torchdrug

  A powerful and flexible machine learning platform for drug discovery

  Language:Python1.5k200

• drorlab/DIPS

  Database of Interacting Protein Structures (DIPS)

  Language:Python9614

• ChenPy00/PPB-Affinity

  Baseline model for PPB-Affinity benchmark data

  Language:Jupyter Notebook161

• shenwei356/seqkit

  A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

  Language:Go1.3k160

• DeepGraphLearning/GearBind

  Pretrainable geometric graph neural network for antibody affinity maturation

  Language:Python415

• MutonAI/Mu-Former

  Language:Python182

• CAODH/SurfDock

  SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction

  Language:Python1136

• programmablebio/pepmlm

  Target Sequence-Conditioned Generation of Peptide Binders via Masked Language Modeling

  Language:Python438

• pengzhangzhi/faplm

  FAPLM: A Drop-in Efficient Pytorch Implementation of Protein Language Models

  Language:Python956

• pyg-team/pytorch_geometric

  Graph Neural Network Library for PyTorch

  Language:Python21.7k3.7k

• brineylab/BALM-paper

  Language:Jupyter Notebook165

• martinpacesa/BindCraft

  User friendly and accurate binder design pipeline

  Language:Python36470

• zaixizhang/PocketGen

  PocketGen (Nature Machine Intelligence 24): Generating Full-Atom Ligand-Binding Protein Pockets

  Language:Python14213

• jwohlwend/boltz

  Official repository for the Boltz-1 biomolecular interaction model

  Language:Python1.5k168

• rampasek/GraphGPS

  Recipe for a General, Powerful, Scalable Graph Transformer

  Language:Python691124

• CarbonMatrixLab/AbX

  Official open-source of Antibody Design Using a Score-based Diffusion Model Guided by Evolutionary, Physical, and Geometric Constraints

  Language:Python232

• MinkaiXu/AliDiff

  NeurIPS24: Aligning Target-Aware Molecule Diffusion Models with Exact Energy Optimization

  Language:Python19

• JackYang825/network-prunning

  2

• lucidrains/frame-averaging-pytorch

  Pytorch implementation of a simple way to enable (Stochastic) Frame Averaging for any network

  Language:Python481

• jax-ml/jax

  Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

  Language:Python30.9k2.8k

• bytedance/Protenix

  A trainable PyTorch reproduction of AlphaFold 3.

  Language:Python78362

• drorlab/gvp-pytorch

  Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure

  Language:Python25650

• google-deepmind/alphafold3

  AlphaFold 3 inference pipeline.

  Language:Python5.7k675

• Ced3-han/PepFlowww

  Full-Atom Peptide Design based on Multi-modal Flow Matching (ICML 2024)

  Language:Jupyter Notebook5510

• Graph-and-Geometric-Learning/Frame-Averaging-Transformer

  Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer, NeurIPS2024

  Language:Python223

• general-molecular-simulations/so3lr

  SO3krates and Universal Pairwise Force Field for Molecular Simulation

  Language:Python683

• Lightning-AI/pytorch-lightning

  Pretrain, finetune ANY AI model of ANY size on multiple GPUs, TPUs with zero code changes.

  Language:Python28.7k3.4k