Tox Dock Server Documentation







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

Tips:

  1. The peptide must be the final chain in your PDB file. For example, if your system consists of three chains (two of which belong to your receptor and one of which is the peptide), the receptor chains can be called "A" and "B" and the peptide "K." More information on how to do this simply in PyMOL is available at: https://pymolwiki.org/index.php?title=Alter&redirect=no.

  2. 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.

  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).

  4. 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.

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

  6. Download a few of the top models and inspect them visually to ensure they are reasonable.

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

  8. If you want to get an average "score" for your peptide to compare to other peptides, refer to the "average reweighted_sc for top 25 models" score listed on the Results page. 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, A. E., Kuryatov, A., Zebroski, H. A., Powell, S. R., Filipenko, P., Hussein, A. K., . . . Holford, M. (2017). Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1703952114


  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. The Rosie implementation was developed by Sergey Lyskov in GrayLab@JHU.