An opinionated list of awesome Python frameworks, libraries, software and resources.

💫 Industrial-strength Natural Language Processing (NLP) in Python

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

MDAnalysis is a Python library to analyze molecular dynamics simulations.

torchbearer: A model fitting library for PyTorch

MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

A deobfuscator for PyArmor.

Collection of Pytorch lightning tutorial form as rich scripts automatically transformed to ipython notebooks.

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

Plausibility checks for generated molecule poses.

MoleculeKit: Your favorite molecule manipulation kit

Antibody Numbering and Antigen Receptor ClassIfication

Benchmarking common tasks on proteins in various languages and packages

Exploring microbial patterns through subtle nucleotide variation within 16S rRNA gene tag sequences of closely related taxa

[IEEE Trans. AI 2024] Spiking Diffusion Models

ProtVec can be used in protein interaction predictions, structure prediction, and protein data visualization.

Scores for Hydrophobicity and Charges based on SASAs

A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations