📖 Table of contents
💡 Notes
- The following lists are curated by humans, as such may be incomplete
- We do not wish to advertize one tool over any other, but simply list the tools we are aware of in a random order
- Any suggestions for improvements and additions are welcome as issues or pull requests
- Projects we identify as discontinued are marked with 💀 and in a section at the end
- If you wish to include this list in a publication do so by using the link "https://github.com/biolists/biodiffusion"
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Methods that from noise sample protein structures, e.g. backbones.
- RFDiffusion
- Backbone diffusion
- Chroma
- Backbone diffusion
- FoldingDiff
- Torsion angle diffusion
- FrameDiff
- Backbone diffusion
- Genie
- Backbone diffusion
Methods that from noise sample sequences, e.g. residue unmasking.
- NOS
- Masked residue inpaining
- EvoDiff
- Masked residue inpaining, conditioned on MSA or single sequence
- GraDe-IF
- Inverse protein folding: from structure to sequence
Methods that, given an input in modality X, impute a structure output, e.g. from image domain to PDB structure.
- CryoDRGN
- CryoEM structure reconstruction
Methods that operate on two molecules and predict an aspect of bidning, e.g. pose
- DiffDock
- Small molecule binding pose
- DiffDock-PP
- Protein-protein binding pose
- NeuralPLexer
- Small molecule binding
- DynamicBind
- Find binding pockets on protein surfaces
- NOTE: no code available @ GitHub repo
Methods that generate some entity (e.g. small mol) linking or binding an input entity/entities (e.g. linker generation)
- DiffLinker
- Linker generation
- DiffSBDD
- Small molecule generation given pocket
- DiffAB
- Design antibody given antigen structure
- DiffBP
- Small molecule generation given pocket
- ProtDiff_SMCDiff
- C-alpha backbone diffusion
- According to GitHub, superseeded by FrameDiff and RFdiffusion
