yx0516

yx0516's Stars

• google-deepmind/alphafold3

  AlphaFold 3 inference pipeline.

  Language:Python5.9k52227705

• biopython/biopython

  Official git repository for Biopython (originally converted from CVS)

  Language:Python4.5k1701.7k1.8k

• jwohlwend/boltz

  Official repository for the Boltz-1 biomolecular interaction model

  Language:Python1.5k31105188

• chaidiscovery/chai-lab

  Chai-1, SOTA model for biomolecular structure prediction

  Language:Python1.5k23139193

• bytedance/Protenix

  A trainable PyTorch reproduction of AlphaFold 3.

  Language:Python852193875

• kyegomez/AlphaFold3

  Implementation of Alpha Fold 3 from the paper: "Accurate structure prediction of biomolecular interactions with AlphaFold3" in PyTorch

  Language:Python768256104

• martinpacesa/BindCraft

  User friendly and accurate binder design pipeline

  Language:Python4091114475

• RosettaCommons/protein_generator

  Joint sequence and structure generation with RoseTTAFold sequence space diffusion

  Language:Python292142047

• ngruver/NOS

  Protein Design with Guided Discrete Diffusion

  Language:Python121101010

• amyxlu/cheap-proteins

  Joint embedding of protein sequence and structure with discrete and continuous compressions of protein folding model latent spaces. http://bit.ly/cheap-proteins

  Language:Python103358

• westlake-repl/SaprotHub

  SaprotHub: Making Protein Modeling Accessible to All Biologists

  Language:Jupyter Notebook854118

• AstraZeneca/DiffAbXL

  The official implementation of DiffAbXL benchmarked in the paper "Exploring Log-Likelihood Scores for Ranking Antibody Sequence Designs", formerly titled "Benchmarking Generative Models for Antibody Design".

  Language:Python63546

• data2code/afpdb

  Efficient manipulation of protein structures in Python

  Language:Jupyter Notebook50303

• DeepGraphLearning/GearBind

  Pretrainable geometric graph neural network for antibody affinity maturation

  Language:Python41565

• minmarg/gtalign_alpha

  GTalign, HPC protein structure alignment, superposition and search (alpha release)

  Language:Cuda39313

• piercelab/tcrmodel2

  Language:Python364216

• TencentAI4S/HuDiff

  Code for humanization of antibody and nanobody

  Language:Python32351

• microsoft/peft_proteomics

  LoRA for protein language models

  Language:Jupyter Notebook31322

• KULL-Centre/_2023_Blaabjerg_SSEmb

  Language:Jupyter Notebook30102

• TencentAI4S/IgGM

  Language:Python27204

• oxpig/PLAbDab

  The Patent and Literature Antibody Database (PLAbDab): an evolving reference set of functionally diverse, literature-annotated antibody sequences and structures

  Language:Jupyter Notebook23104

• jianlin-cheng/DRLComplex

  Deep reinforcement learning for protein complex modeling

  Language:Python12213

• regeneron-mpds/propermab

  Language:GLSL121

• PNUMLB/AptaTrans

  AptaTrans Pipeline

  Language:Python11153

• minghuilab/PremPLI

  Language:Rich Text Format8223

• nohandsomewujun/FlowDesign

  Language:Python7211

• prody/DruGUI

  Druggability Suite

  Language:Tcl6578

• zlisysu/CS-FEP_run

  A demo of Combined structure free energy perturbation (CS-FEP) approach

  Language:Shell6203

• BiGCAT-UM/PSnpBind-ML-notebook

  Language:Jupyter Notebook5002

• ZheLi-Lab/The_CAR_enhanced_adaptive_sampling_method

  The convergence-adaptive roundtrip enhanced sampling method that enables rapid and accurate FEP calculations.

  Language:Python51