GOBSMACKED: prepare a run

1. Protein

UniProt accession, PDB ID or sequence Force a particular PDB entry as the starting structure (optional)

Filled in, this is a redocking control: the run starts from the crystal it is judged against, which is the standard positive control and the quickest way to see the app work. Clear it to start from the AlphaFold model instead, which is the harder and more realistic test.

Or drop your own coordinates (.pdb, .cif) Trim to a domain, optional (first-last residue)

Leave this empty for a crystal structure: it is already the domain. It is for a full-length predicted model, where solvating the other 950 residues costs an order of magnitude in MD time and tells you nothing about the pocket. Whatever you put here must be in the same numbering as the pocket, which is the structure's own: a crystal often counts from the mature protein and UniProt from the precursor, and for EGFR those differ by 24. The bundle is refused if the range would cut into the pocket.

Co-fold the receptor with your ligand first (Boltz-2)

Folds the protein and the ligand together, then throws the ligand away and docks it back into the pocket that was built around it. On the five-structure comparison this was the only starting point whose top-ranked pose was the right one (1.40 Å at rank 1, against 4.29 to 8.77 Å for a crystal, an AlphaFold model and an ESMFold model) and the only run to grade B. Its own predicted ligand pose was 4.5 to 4.8 Å out, which is why the pocket is kept and the ligand re-docked rather than believed. Adds roughly 15 minutes to the run and needs the GPU machine. The structure fetched above is still used to pick the pocket and size the box.

Family, filled in by Fetch

Pfamnot fetched

2. Sequence and annotation

3. Ligand

Name SMILES

pH

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.

Reference PDB entry

Search below and click an entry, or type one here.

Apo reference, optional: the same protein with nothing bound

5. Pocket

Residues (chain:number, comma separated)

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.

6. Run settings and bundle

Docking

Poses

Production MD (ps)

Frame every (ps)

Affinity Predict affinity with Boltz-2

Scores the docked pose and the relaxed complex, and reports both. Adds a few minutes and a one-off download.

Frames scored after MD

Five frames across the last fifth of the run, reported as a mean and a spread.

Title for the Runs table Visibility

This run appears in the Runs tab for anyone.