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Reference docs for subseq.bio programs and API.
Core
Program Guides
RF DiffusionBackbone generation with contigs or symmetry.
RFdiffusion3All-atom RFdiffusion3 design workflows.
AlphaFold 2Structure prediction presets.
OpenFold3Biomolecular structure prediction.
Chai-1Chai-1 structure prediction.
ESMFold2All-atom structure prediction.
ESMCProtein embeddings and sequence scoring.
ESMfoldSequence-to-structure folding.
Evo 2DNA generation, sequence scoring, and embeddings.
BioEmuMonomer ensemble sampling and side-chain reconstruction.
LigandMPNNSequence design conditioned on ligands.
Boltz-2Structure and affinity prediction.
BoltzGenBinder design diffusion pipeline.
MMseqs2MSA and search templates.
DiffDock-LLigand docking from SMILES/SDF.
DiffDock-PPProtein–protein docking baseline.
Shape-CompProtein interface shape complementarity.
GROMACSMD command examples.
Beautiful AtomsBlender/Cycles molecular renders and animations.
PyMOL+Batch renders and animations.
OpenMMPython minimization starter.
FreeBindCraftDe novo binder search settings.
UtilityRun custom scripts in a slim image.