Using anchoring motifs for the computational design of protein-protein interactions.
Jacobs TM, Kuhlman B. Biochem Soc Trans. 2013 Oct 1;41(5):1141-5.
Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.
Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, Kirshenbaum K, Arora PS, Das R, Bonneau R. PLoS One. 2013 Jul 15;8(7):e67051
Interpreting your results:
The energies, structure and sequence output by RosettaDesign are placed in a pdb file.
The pdb file has the following sections:
1) coordinates of the design structure
2) a table of energies for each residue in the protein: totals are at the bottom
fa_atr attractive portion of the Lennard Jones potential fa_rep repulsive portion of the Lennard Jones potential fa_sol Lazaridis-Karplus solvation energy fa_intra_rep internal (within residue) Lennard Jones repulsive energy pro_close proline closure energy fa_pair pairwise electrostatics term derived from statistics on the pdb database hbond_sr_bb hbond energy, short-range backbone-backbone hbond_lr_bb hbond energy, long-range backbone-backbone hbond_bb_sc hbond energy, backbone-sidechain hbond_sc hbond energy, sidechain-sidechain dslf_ss_dst disulfide energy terms dslf_cs_ang dslf_ss_dih dslf_ca_dih rama ramachandran torsion energy derived from statistics on the PDB omega omega angle energy fa_dun rotamer energy derived from statistics on the PDB p_aa_pp aa preference term; probability of seeing a given aa at given phi and psi angles ref reference energy for this residue total total energy for this resiude
For a more detailed description of how to interpret your results, please see the Rosetta release manual page.
In some cases RosettaDesign does appear to make odd choices, and it helps to know beforehand what some of these tendencies are. In these situations it is probably best to use a resfile to try and point Rosetta away from these pitfalls.
1) The program likes to put amino acids with similar chemical properties near each other. This is primarily because polar residues can hydrogen bond with each other, while hydrophobics can pack against each other giving favorable attractive and solvation energy. The result is that in some cases you may observe a large cluster of hydrophobic residues on the surface of a protein, or a cluster of polars in the core. In some cases this can be avoided by forcing key residues to be polar or hydrophobic.
2) Sometimes polar groups are buried without a hydrogen bonding partner. The energy function has been parameterized to avoid this, but there is no filter that prevents it.
1. Can RosettaDesign calculate the energy of the native protein without doing any design?
Yes, if you specify a resfile which has NATRO as the default behaviour, RosettaDesign will just score the uploaded structure and no do any design on it.
2. What does "Can't find starting residue in PDB file" mean in the log file?
The error message "Can't find starting residue in PDB file" usually means that your uploaded files format is not a typical PDB file so the server cannot process your structure.
3. What is "unrecognized residue:"?
RosettaDesign reads the three letter representation of each amino acid from the PDB file. If a residue is not one of the canonical 20 amino acid types and also has not been entered into Rosetta, this error message may occur. The easiest solution is to remove these non-canonical residues from your PDB file and resubmit.
4. What is "missing backbone atoms"?
The error message "missing backbone atoms" means there are backbone atoms in the PDB file which are missing. RosettaDesign will try to rebuild these atoms from ideal versions of the amino acids to complete the run.