Tools

• • ColabFold - Making protein folding accessible to all via Google Colab

  • ColabDesign - Design proteins using TrRosetta, RosettaFold and AlphaFold

  • SMURF - End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman

  • AF2Rank - State-of-the-Art Estimation of Protein Model Accuracy using AlphaFold

  • GREMLIN  - Web-server and database for predicting contacts.

    • For source code see: C++, Python (Tensorflow), Python (Jax)

  • seqsal - What do generative models learn from protein sequences?

  • seqmodels - Unified framework for modeling multivariate distributions in biological sequences

  • map_align - contact map alignment

  • AF2BIND - Lightweight and fast prediction of ligand-binding sites