The RosettaDock protein-protein docking server predicts the structure of protein complexes given the structures of the individual components and an approximate binding orientation. The server uses the Rosetta 2.1 protein structure modeling suite.
Please cite the following articles when referring to results from our server:
- Lyskov S., Gray J.J.
"The RosettaDock server for local protein-protein docking"
Nucleic Acids Research 2008; doi: 10.1093/nar/gkn216
- 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).
Complete source code for RosettaDock is available by license from RosettaCommons.
Practical applications of the method are detailed in the following papers, including results from the blind prediction challenge known as
CAPRI:
- 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.