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

TensorFlow-based neural network library

Sequential regulatory activity predictions with deep convolutional neural networks.

deep residual neural network for classifying the pathogenicity of missense mutations.

↘️↗️↩️ Scalable protein quaternary structure alignment algorithm

Search protein structural motifs in the PDB.

Code for the MSB publication: Exploring amino acid functions and positional subtypes in a deep mutational landscape

R package for annotating deep mutational scanning data using the deep mutational landscape

Making Protein folding accessible to all!

A tool for accurate prediction of a protein's secondary structure from only it's amino acid sequence

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

A console-based alignment viewer

A generative latent variable model for biological sequence families.

Scripts to analyse the sequence composition and bias of protein and nucleotide sequences.

Scripts to calculate sequence similarity networks (SSNs) and clustering of protein sequences.

C-library for calculating Solvent Accessible Surface Areas

Protein Graph Library

Benchmarking common tasks on proteins in various languages and packages

2D and 3D molecular visualization in Jupyter notebooks using 3DMol.js and D3.js

Notebook-integrated tools for molecular simulation and visualization

Jupyter widget to interactively view molecular structures and trajectories

🧬 An R package for visualizing molecular data in 3D

Information to the 3,542 identified Fibrillar Adhesins-like proteins

Code for phylogenetic analyses of protein domains

Attempt at reproduction of AlphaFold2

Software for discovery of compositional biases in proteins

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