Symmetric Docking Server Documentation



The SymDock protocol predicts the structure of symmetric homooligomeric protein assemblies starting from the structure of a single subunit. It is very similar in spirit to the standard protein-protein docking protocol and contains the same basic components. The relative subunit orientation and conformations of side-chains are simultaneously optimized for a symmetric protein assembly. In contrast to the ROSIE docking server, the SymDock server does a global search for best docking orientation (5000 or 10 000 models, depending on symmetry type).

Inputs

The input is a monomeric subunit structure. The SymDock server currently supports two types of symmetries, cyclical (Cn) and dihedral (Dn) symmetry. The total number of subunits in the assembly has to be specified. With 4 subunits and cyclical symmetry that becomes a C4 symmetric tetramer, while 4 subunits with dihedral symmetry becomes a D2 tetramer. To limit computational cost no more than 10 subunits can be simulated with the server interface to SymDock.

Tips

Interpreting Results


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

  1. Andre I, Bradley P, Wang C, Baker D. Prediction of the structure of symmetrical protein assemblies. Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17656-61.
    Link: http://www.pnas.org/content/104/45/17656.long [this is the primary citation for the algorithm].

  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

More information on how to run the SymDock application stand-alone can be found in:

DiMaio F, Leaver-Fay A, Bradley P, Baker D, André I. Modeling Symmetric Macromolecular Structure in Rosetta3 PLoS One. 2011;6(6):e20450. doi: 10.1371/journal.pone.0020450. link: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0020450



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

  1. Andre I, Bradley P, Wang C, Baker D. Prediction of the structure of symmetrical protein assemblies. Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17656-61.
    Link: http://www.pnas.org/content/104/45/17656.long [this is the primary citation for the algorithm].

  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.


Modeling tools developed by André lab. The Rosie implementation was developed by Sergey Lyskov and Malte Johansson.