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ab_rmsd

Calculate the RMSD between two antibody structure (including nanobody and antibody).

abgnn

PyTorch code for KDD 2023 paper "Pre-training Antibody Language Models for Antigen-Specific Computational Antibody Design"

ai2bmd

AI-powered ab initio biomolecular dynamics simulation

airs

Artificial Intelligence for Science (AIRS)

awesome-diffusion-models-for-science

awesome-hypergraph-network

A curated list of Hypergraph Learning, Hypergraph Theory, Hypergraph Dataset and Hypergraph Tool.

awesome-pretrain-on-molecules

[IJCAI 2023 survey track]A curated list of resources for chemical pre-trained models

awesome-self-supervised-gnn

Papers about pretraining and self-supervised learning on Graph Neural Networks (GNN).

bio-diffusion

A PyTorch hub of denoising diffusion probabilistic models designed to generate novel biological data

cafa-5-protein-function-prediction

Protein Function Prediction competition on Kaggle

cafa5

chatpaper

Use ChatGPT to summarize the arXiv papers. 全流程加速科研，利用chatgpt进行论文全文总结+专业翻译+润色+审稿+审稿回复

chemprop

Message Passing Neural Networks for Molecule Property Prediction

chroma

A generative model for programmable protein design

cs224n-2019-solutions

Complete solutions for Stanford CS224n, winter, 2019

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

difformer

The official implementation for ICLR23 spotlight paper "DIFFormer: Scalable (Graph) Transformers Induced by Energy Constrained Diffusion"

dig

A library for graph deep learning research

drugbank

drugbank相关数据的处理，包括获取药物sdf结构文件，drug相关信息，drug作用相关蛋白信息，drugbank中drug id与其他数据库的映射，protein蛋白相关信息到其他数据库的映射

drugvqa

Predicting Drug Protein Interaction using Quasi-Visual Question Answering System

dymean

This repo contains the codes for our paper "End-to-End Full-Atom Antibody Design"

echognn

Graph Neural Networks for Explainable Ejection Fraction Estimation

equiformer

[ICLR'23 Spotlight] Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs

equiformer-pytorch

Implementation of the Equiformer, SE3/E3 equivariant attention network that reaches new SOTA, and adopted for use by EquiFold for protein folding

equiformer_v2

[arXiv'23] EquiformerV2: Improved Equivariant Transformer for Scaling to Higher-Degree Representations

fabind

FABind: Fast and Accurate Protein-Ligand Binding (NIPS 2023)

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

gnnpapers

Must-read papers on graph neural networks (GNN)

graph-neural-networks-for-drug-discovery

graphchem

Graph-based machine learning for chemical property prediction