GOBSMACKED: prepare a run

1. Protein

UniProt accession, PDB ID or sequence Force a particular PDB entry as the starting structure (optional) Or drop your own coordinates (.pdb, .cif) Trim to a domain, optional (first-last residue)

3. Ligand

Name SMILES

Run settings

Docking

Poses

Production MD (ps)

Frame every (ps)

Title for the Runs table Visibility

This run appears in the Runs tab for anyone.

Scope

Fetch a protein to see it here.

Click residues in the structure or the sequence track to build the pocket. The box is the selection's extent plus 8 A, floored at 18 A per side.

2. Sequence and annotation

Pocket

Residues (chain:number, comma separated)

Family

Pfamnot fetched

4. Reference structure

Ranked by how similar each entry's ligand is to yours. A crystal holding the same ligand is preferred over a sharper one holding a different chemotype.

Apo reference, optional: the same protein with nothing bound