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In Sandbox, click New Prediction to get started, or Use CLI for instructions on using the API. Sandbox New After naming your prediction with an identifiable description, add polymers, small molecules and cofactors to be included in the complex. Image

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Adding Components

Import a .cif file or provide an RCSB PDB code to load all protein, RNA and DNA sequences, ligands and cofactors present in the file.
Import small molecules using a SMILES string, the structure drawer, or from an RCSB CCD code.
Add protein, RNA and DNA sequences individually from UniProt or FASTA strings. Modified amino acids and nucleic acids can be specified when adding a sequence.

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Constraints

On the Constraints page, add any bond, contact or pocket-contact information to guide the prediction. Alternatively, skip this step to continue without constraints.
Constraint TypeDescription
BondSpecify a covalent bond between atoms in the complex. Important for covalent ligands or cyclic proteins.
ContactSpecify a maximum distance (4-20 Å) between a pair of atoms as a hint to the model.
PocketSpecify residues that a particular binder chain must be within a certain distance from.
Please see our dedicated Constraints documentation for full details

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Affinity Prediction

The Affinity page lets you select a ligand to calculate binding affinity for ligand-protein interactions, or skip this step to run a structure-only prediction. Image
Only ligands with exactly one copy are allowed for affinity calculation.
When you’re ready, click Submit Prediction.