Tools

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

  • ColabDesign - Design proteins using TrRosetta, RosettaFold and AlphaFold

  • BindCraft - One-shot design of functional protein binders

  • MSA_Pairformer - Scaling down protein language modeling with MSA Pairformer

  • BoltzDesign - Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design

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

  • SoftAlign - End-to-end protein structures alignment

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

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

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

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

  • CatJac - Categorical Jacobian to uncover pairwise relationships in sequence smodels

    • Implemented for: ESM2, ESM3, ProteinMPNN, Evo, gLM2

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

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

  • map_align - contact map alignment