Generative model for protein binder design for protein and small molecule targets. Combines a pretrained flow-based generative model (built on La-Proteina) with inference-time optimization.

HalluDesign, a hallucination-driven all-atom framework for the iterative co-optimization and co-design of protein sequences and structures by leveraging the forward pass of a structure prediction m…

WYSIWYG cryo-em mask maker

Official repository of "ODesign: A World Model for Biomolecular Interaction Design"

A diffusion-based ML model for de novo design of DNA, RNA, proteins, and mixed assemblies.

An IPython/Jupyter widget for interactive molecular visualization, based on Molstar. This is the Jupyter widget version of nano-protein-viewer.

A fully open source biomolecular structure prediction model based on AlphaFold3

User friendly and accurate binder design pipeline

BindCraft modified to make PyRosetta use and installation optional: no license needed

Making Protein Design accessible to all via Google Colab!

This API provides programmatic access to the AlphaGenome model developed by Google DeepMind.

It's a package for evaluation of predicted poses, right?

protein structure generation with sparse all-atom denoising models

Scoring function for interprotein interactions in AlphaFold2 and AlphaFold3

Inference code for scalable emulation of protein equilibrium ensembles with generative deep learning

A Python implementation of the MRC2014 file format

A comprehensive foundation model for cryo-EM image processing

Fast indexing and search of discontinuous motifs in protein structures

A comprehensive library for computational molecular biology

Colab Notebooks covering deep learning tools for biomolecular structure prediction and design

Official repository for the Boltz biomolecular interaction models

AlphaFold 3 inference pipeline.

Multiple Protein Structure Alignment at Scale with FoldMason

PINDER: The Protein INteraction Dataset and Evaluation Resource

Dataset and package for working with protein-protein interactions in 3D