Tox Dock Server Documentation







Overview: ToxDock is an application geared towards docking toxin peptides to homology models of ion channels

Tips:

  1. 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.

  2. 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)

  3. 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.

  4. Remove ions, co-factors, ligands, etc. from your structure

  5. Sort the outputs by reweighted_sc and inspect the top models visually.

  6. The peptide should be positioned close to where you think it docks to get a reasonable answer. This is not a global docking algorithm.

  7. 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 analysis.



Inputs:



Please cite the following article when referring to results from our ROSIE server:

  1. Leffler al., Computational and evolutionary design of selective peptide antagonists of ion channels in the absence of crystal structures. In preparation.


  2. 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. Link

We welcome scientific and technical comments on our server. For support please contact us at Rosetta Forums with any comments, questions or concerns.


The ToxDock Modeling tool developed by Abba Leffler in the Holford, Rudy, and Bonneau labs. The Rosie implementation was developed by Sergey Lyskov in GrayLab@JHU.