Since the release of Alphafold2, there have been a lot of open-source tools that were released to facilitate in-silico experiments with protein structures. This list contains all the open-source tools that have been released so far. I will try to keep the list updated. PRs are welcome.
- ALBATROSS: An easy-to-use deep-learning tool for predicting 3D properties of disordered proteins from sequence, Nature Methods, 2024. [paper] [code]
- Predicting multiple conformations via sequence clustering with AlphaFold2, Nature,2023. [paper] [code]
- AlphaFill. [paper] [code]
- AlphaFind: Discover structure similarity across the entire known proteome. [website] [code]
- AlphaFold Meets Flow Matching for Generating Protein Ensembles. [paper] [code]
- Chroma: A generative model for programmable protein design [paper] [code]
- Evo: DNA foundation modeling from molecular to genome scale [paper] [code]
- Fragfold: igh-throughput computational discovery of inhibitory protein fragments with AlphaFold [paper] [code]
- GlycoSHIELD is a simple MD pipeline to generate realistic glycoprotein models. [paper] [code]
- LightDock is a protein-protein, protein-peptide and protein-DNA docking framework based on the Glowworm Swarm Optimization (GSO) algorithm. [paper] [code]
- NeuralPlexer: A deep generative model to jointly predict protein-ligand complex 3D structures and beyond, Nature intelligence, 2024. [paper] [code]