xinluzhu

af2seq

alphafold

Open source code for AlphaFold.

annotated_deep_learning_paper_implementations

🧑‍🏫 60 Implementations/tutorials of deep learning papers with side-by-side notes 📝; including transformers (original, xl, switch, feedback, vit, ...), optimizers (adam, adabelief, sophia, ...), gans(cyclegan, stylegan2, ...), 🎮 reinforcement learning (ppo, dqn), capsnet, distillation, ... 🧠

chroma

A generative model for programmable protein design

DeCOIL

A computational method to optimize degenerate codons for synthesizing an informed combinatorial mutagenesis protein variant library

DiffDock

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

Diffusional-Fingerprinting

evodiff

Generation of protein sequences and evolutionary alignments via discrete diffusion models

FoldFlow

Code release for our recent paper "SE(3)-Stochastic Flow Matching for Protein Backbone Generation" https://arxiv.org/abs/2310.02391

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

frame-flow

Fast protein backbone generation with SE(3) flow matching.

hydra

Hydra is a framework for elegantly configuring complex applications

ILEE_CSK

masif_seed

Masif seed paper repository

MolecularNodes

Addon and nodes for working with structural biology and molecular data in Blender.

MULTICOM3

The software system of predicting protein tertiary and quaternary structures. It is prepared for CASP15 by BMLab.

netron

Visualizer for neural network, deep learning and machine learning models

ProteinMPNN

Code for the ProteinMPNN paper

Python

最良心的 Python 教程：

pytorch_geometric

Graph Neural Network Library for PyTorch

PytorchGeometricTutorial

Pytorch Geometric Tutorials

rf_diffusion_all_atom

Public RFDiffusionAA repo

RFdiffusion

Code for running RFdiffusion

se3-transformer-public

code for the SE3 Transformers paper: https://arxiv.org/abs/2006.10503

TARDIS-public

Public releases of TARDIS

Treadmilling-Speed-Analysis

Automated image analysis protocol to quantify the velocities of dynamic protein filaments

udlbook

Understanding Deep Learning - Simon J.D. Prince

Umol

Protein-ligand structure prediction

walk-jump

Official repository for discrete Walk-Jump Sampling (dWJS)

x-transformers

A simple but complete full-attention transformer with a set of promising experimental features from various papers