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. 2008 Jul 1;36(Web Server issue):W233-8.
doi: 10.1093/nar/gkn216. Epub 2008 Apr 28.

The RosettaDock server for local protein-protein docking

Sergey Lyskov  1 , Jeffrey J Gray
Affiliations

The RosettaDock server for local protein-protein docking

Sergey Lyskov et al. Nucleic Acids Res. .

Abstract

The RosettaDock server (http://rosettadock.graylab.jhu.edu) identifies low-energy conformations of a protein-protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations. The server requires two protein structures as inputs and a starting location for the search. RosettaDock generates 1000 independent structures, and the server returns pictures, coordinate files and detailed scoring information for the 10 top-scoring models. A plot of the total energy of each of the 1000 models created shows the presence or absence of an energetic binding funnel. RosettaDock has been validated on the docking benchmark set and through the Critical Assessment of PRedicted Interactions blind prediction challenge.

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Figures

Figure 1.
Figure 1.
Sample results page. In this example, all 10 low-energy conformations are similar and the score versus r.m.s.d. plot exhibits a binding funnel at ∼1 Å from the starting input conformation.
Figure 2.
Figure 2.
System architecture.
See this image and copyright information in PMC

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