Protein
IQ
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Protein
IQ
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Batch setup
Tool
AF2Dock
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Inputs
Template
CSV / Excel
Paste CSV
Inputs
Structures and residue mappings
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Receptor
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or drag and drop
PDB, CIF · up to 50 MB
Ligand protein
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or drag and drop
PDB, CIF · up to 50 MB
Receptor MSA
Ligand MSA
Sampling parameters
Number of samples
Flow-matching steps
Merge first steps
Additional refine steps
Runtime options
Random seed
Model checkpoint
AF2Dock base
Native experiment configuration
Input pLDDT filtering
Filter low-pLDDT residues
pLDDT cutoff
Minimum residues
Minimum residue ratio
Intermediate outputs
Save all templates
Save intermediate predictions
Save intermediate confidence files
Batch pairing
All combinations
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