Aroop Sircar - RosettaAntibody: Antibody Variable Region Homology Modeling Server

Version 1

      Publication Details (including relevant citation   information):

      Aroop Sircar, Eric T. Kim, Jeffrey J. Gray

      Nucleic Acids Research 37(Web Server Issue), W474-W479, April 29,   2009.

      Abstract:

      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.

      Address (URL): http://dx.doi.org/10.1093/nar/gkp387