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biopython

Official git repository for Biopython (originally converted from CVS)

biotite

A comprehensive library for computational molecular biology

chroma

A generative model for programmable protein design

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

exper

Exper is a Python package designed for personal use by the author to streamline the execution of PyTorch-based deep learning experiments. This framework is specifically crafted to support Distributed Data Parallel (DDP) training and provides a convenient mechanism for saving experiment logs.

gearnet

GearNet and Geometric Pretraining Methods for Protein Structure Representation Learning (https://arxiv.org/abs/2203.06125)

geometric-rna-design

gRNAde: Geometric Deep Learning for RNA Design

mlx-examples

Examples in the MLX framework

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

morn

MORN: Molecular Property Prediction Based on Textual-Topological-Spatial Multi-View Learning.

mrz-zz

Config files for my GitHub profile.

mrz-zz.github.io

nobelium

A static blog build on top of Notion and NextJS, deployed on Vercel.

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

paddlehelix

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.

pytorch_geometric

Graph Neural Network Library for PyTorch

rdkit

some scripts for RDKit

ruleset

torchdrug

A powerful and flexible machine learning platform for drug discovery