ROSIE Docking Server Documentation

Tips:

The RosettaDock Server performs a local docking search. That is, the algorithm will search a set of conformations near the given starting conformation for the optimal fit between the two partners. Some suggestions:

  1. You must upload a reasonable guess for the starting position. Place the protein partners near contact (but not overlapping) with the relevant patches of the proteins facing each other.

  2. PyMol can be a useful tool to position proteins relative to each other. Use "editing" mode from the right panel, and try right-clicking to select a chain and "drag" to enable translation and rotation of the molecule (typically requiring left-shift + middle and left buttons). Finally from the main menu, File→Export Molecule can be used to write a PDB file containing the starting structure with both docking partners. The ‘align’ command may also be helpful if you are using a homologous complex as a guide.

    Alternately, starting positions can be creating using one of several docking servers which perform global searches. Some leading servers include ClusPro, GRAMM-X, HEX, PatchDock, SymmDock, ZDOCK. Note that coordinate file formats from these servers might need to be brought into compliance for use by our server (e.g., putting a TER record between docking partners, assuring that the occupancy field is present and standard atom and residue names are used, etc.).

  3. Docking partners can be uploaded as two separate PDB files or a single PDB file. If there are multiple chains which serve as a single docking partner (e.g., the heavy and light chains of an antibody), the TER line should be removed between the two chains so that Rosetta knows to treat these as a single partner. Similarly, when creating a combined single input file with both partners, place a TER line between the two partners.

  4. RosettaDock’s local perturbation includes ~ ±3 Å in the direction between the two proteins, ~ 8 Å in the directions sliding the proteins relative to each other along their surfaces, ~ 8° of tilt of the proteins, and a complete 360° spin around the axis between the centers of the two proteins. The server will start 1000 independent simulations from this range of random positions.

  5. Given the local nature of the search, there is no need to include extra domains of the proteins beyond the two interacting domains. Trim unneeded residues out of your PDB file before uploading. The server will not accept PDBs larger than 600 residues total.

  6. A fundamental assumption exploited by RosettaDock is that protein backbone conformations typically do not change much upon association. This holds for many proteins, but not all. If you believe that the backbone of one of your partners is flexible, you should be cautious with the results. For example, docking of a short, flexible peptide (~10 residues) is not likely to work, since a peptide lacks the tertiary interactions which stabilize full-size domains (75-250 residues). Similarly, docking will not capture the flexibility of a molecule like calmodulin; the correct backbone of the protein must be uploaded to begin. Docking of a single amino acid will not produce a reasonable result and is not allowed by the server.

  7. The PDB file format description can be found here.

  8. RosettaDock requires all backbone atoms to be present for any residue which appears in the starting structure (missing side-chains are acceptable since they will be rebuit). The error message "missing backbone atoms" means there are one or more backbone atoms missing in the input pdb file(s).

Interpreting Results

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.


We welcome scientific and technical comments on our server. For support please contact us at Rosetta Forums with any comments, questions or concerns.


Happy docking!