Nucleic Acids Research Advance Access originally published online on May 20, 2009
Nucleic Acids Research 2009 37(Web Server issue):W474-W479; doi:10.1093/nar/gkp387
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W474-W479
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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RosettaAntibody: antibody variable region homology modeling server
1Department of Chemical and Biomolecular Engineering, 2Department of Biomedical Engineering and Department of Computer Science, 3Program in Molecular Biophysics and 4Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
*To whom correspondence should be addressed. Tel: +1 410 516 5313; Fax: +1 410 516 5510; Email: jgray{at}jhu.edu
Received January 22, 2009. Revised April 15, 2009. Accepted April 29, 2009.
The RosettaAntibody server (http://antibody.graylab.jhu.edu) predicts the structure of an antibody variable region given the amino-acid sequences of the respective light and heavy chains. In an initial stage, the server identifies and displays the most sequence homologous template structures for the light and heavy framework regions and each of the complementarity determining region (CDR) loops. Subsequently, the most homologous templates are assembled into a side-chain optimized crude model, and the server returns a picture and coordinate file. For users requesting a high-resolution model, the server executes the full RosettaAntibody protocol which additionally models the hyper-variable CDR H3 loop. The high-resolution protocol also relieves steric clashes by optimizing the CDR backbone torsion angles and by simultaneously perturbing the relative orientation of the light and heavy chains. RosettaAntibody generates 2000 independent structures, and the server returns pictures, coordinate files, and detailed scoring information for the 10 top-scoring models. The 10 models enable users to use rational judgment in choosing the best model or to use the set as an ensemble for further studies such as docking. The high-resolution models generated by RosettaAntibody have been used for the successful prediction of antibody–antigen complex structures.