SnugDock Server Documentation

Overview: This app is the ROSIE interface to the Rosetta SnugDock program for antibody-antigen docking.

Briefly, SnugDock expands on the standard RosettaDock approach to predict antibody-antigen complexes through optimization of antibody degrees of freedom relevant to binding. SnugDock, like RosettaDock, consists of two stages. The first is a low resolution, local docking, stage where conformations near by the starting conformation are sampled. Beyond regular docking, SnugDock explicitly refines the antibody CDR H3/H2 loops. The second stage is a high resolution refinement stage where side chains are reintroduced to the model. Local conformational space is still sampled, but now side chains are also refined. See the reference for a full description of the protocol.

  1. Input should be a single PDB with the antibody-antigen complex in a starting conformation thought to be approximate to the native. The input PDB must be ordered with the light chain coming first, then the heavy chain, and finally the antigen. These chains must then be specified as input.
  2. Input can include homology models, but be aware that the quality of the predicted complex will depend on the quality of the input homology models.
  3. The "thorough" mode includes 6 times more loop modeling steps than the "fast" mode, but has only shown to be slightly superior in terms of prediction quality.
  4. See also RosettaDock documentation for info:

Input: The mandatory input is a single PDB of the antibody-antigen complex ordered as light chain, heavy chain, and antigen, a string specifying the docking partners with the antigen separate by an underscore "LH_G", and a selection of either the "fast" or "thorough" mode which dictates the amount of loop remodeling.

Interpreting Results: The server returns 1000 predictions of antibody-antigen complexes as PDB files and the score file. The reliability of models is strongly depends on the input files (i.e. better results are seen when docking two crystal structures than docking one crystal structure and one homology model than docking two homology models). See the reference for full details.

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

  1. A. Sircar & J. J. Gray, "SnugDock: Paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models," PLoS Comput. Biol. 6(1): e1000644 (2010). Online

  2. Lyskov S., Gray J.J. "The RosettaDock server for local protein-protein docking" Nucleic Acids Research 36 (Web Server Issue), W233-W238 (2008). Online

  3. 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.

Modeling tools developed by GrayLab. The Rosie implementation was developed by Sergey Lyskov.