Rosetta Docking Protocol

[Submit Docking task]

[Docking Queue]

[Docking Server Documentation]

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

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

  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

Methods and practical applications are detailed in the following papers, including results from the blind prediction challenge known as CAPRI:
  • Gray, J.J., Moughan S.E., Wang C., Schueler-Furman O., Kuhlman B., Rohl C.A., Baker D. "Protein-Protein Docking with Simultaneous Optimization of Rigid-Body Displacement and Side-Chain Conformations," J. Mol. Biol. 331(1), 281-299 (2003).

  • Wang, C., Schueler-Furman, O., Baker, D. "Improved side-chain modeling for protein-protein docking," Protein Science 14, 1328-1339 (2005).

  • Sivasubramanian, A., Maynard, J. A. & Gray, J.J. "Modeling the structure of mAb 14B7 bound to the anthrax protective antigen". Proteins vol. 70. 1 (2008). pp. 218-230.

  • Chaudhury S., Sircar A., Sivasubramanian A., Berrondo M., Gray J.J. "Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6–12." Proteins (2007) 69:793–800.

  • Sivasubramanian A., Chao G., Pressler H.M., Witrup K.D., and Gray J.J. "Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis." Structure vol. 14. 3(2006). pp.401-414.

  • Daily M.D., Masica D., Sivasubramanian A., Somarouthu S., and Gray J.J. "CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock," Proteins, 60(2), 181-186 (2005).

  • Gray J.J., Moughon S.E., Kortemme T., Schueler-Furman O., Misura K.M., Morozov A.V., Baker D. "Protein-protein docking predictions for the CAPRI experiment." Proteins (2003) 52:118–122.