Tox Dock Server Documentation
Overview: ToxDock is an application geared towards docking toxin peptides to homology models of ion channels
- The apo pdb should be a crystal structure or model of the target receptor in its
"apo" conformation, without a peptide bound. An example would be using the apo
structure of a potassium channel (PDB: 2R9R) when modeling how a toxin peptide
docks to a homology model of Kv1.3.
- If no apo structure of your channel or receptor exists, search the PDB to see if an
apo structure of a homologous channel or receptor has been crystallized. For
example, when docking to homology models of nicotinic receptors, use the apo
AchBP structure (PDB: 2Y7Y)
- Only standard amino acids are supported at this point. If your peptide has post-
translational modifications, remove them (in PyMOL, for example) and use the
corresponding standard amino acid (e.g. glutamate instead of carboxyglutamate).
Remove N and C terminal modification as well.
- Remove ions, co-factors, ligands, etc. from your structure
- Sort the outputs by reweighted_sc and inspect the top models visually.
- The peptide should be positioned close to where you think it docks to get a
reasonable answer. This is not a global docking algorithm.
- If you want to get an average "score" for your peptide to compare to other
peptides, download the score table and take the mean over the reweighted_sc
column. This is helpful when trying to benchmark your peptides using an ROC type
Peptide/Homology Model complex: A model of the peptide toxin in complex with
Receptor chains: Which chains in your complex correspond to those of the receptor
Peptide chain: Which chain in your complex corresponds to that of your toxin
APO PDB: A model or structure receptor in its apo state (never crystallized with the
Please cite the following article when referring to results from our ROSIE server:
Leffler al., Computational and evolutionary design of selective peptide antagonists
of ion channels in the absence of crystal structures. In preparation.
Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R.,
"Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)".
PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. Print 2013.
We welcome scientific and technical comments on our server. For support please contact us at Rosetta Forums with any comments, questions or concerns.