Frequently asked questions

**If you have specific questions that were not addressed in our about page, help boxes for each submission parameter or here, feel free to write us and we will add them.

  • I submitted a query and received an error. What should I do?
  • Can I submit a structure with lack of density (missing residues)?
  • Can I submit a NMR structure?
  • Can PROSS handle non native amino acids (e.g. Selenomethionine MSE, Carboxylated Lysine KCX etc.)?
  • Is PROSS good for stabilizing symmetric oligomers?
  • Is PROSS good for stabilizing antibodies?
  • Is PROSS good for stabilizing membrane proteins?
  • Is PROSS good for stabilizing small proteins (<100 amino acids)?
  • How much time takes a PROSS calculation?
  • Can I submit a PSE file created by PyMOLl?

I submitted a query and received an error. What should I do?

Checkout our common errors page.


Can I submit a structure with lack of density (missing residues)?

Yes! You may submit a structure that lacks amino acid information, as is typically the case in termini and long/flexible loops.

The missing residues will not be mutated, PROSS is not aware to their existence. In addition, 3 residues from each side (N and C) of the missing stretch will not be mutated either. In the final output however, the designed sequences will include the missing residues to enable direct back translation to DNA and gene ordering. Nevertheless, we strongly recommend that you align the final sequences with the original sequence that you typically use to make sure that there wasn't any problem with the addition of the missing residues (the addition is based on a pairwise alignment of the PDB sequence and the full sequence and rarely residues do not align well).

Can I submit a NMR structure?

No, you can't. You may however, select one of the NMR conformations in the file, delete all others from the file and submit the edited file. However, we strongly recommend avoiding NMR structures as they are typically not accurate enough for these kind of calculations. Use NMR-based structures only when no X-ray structure of your protein target or a close homologue (>95%) is available.

Can PROSS handle non native amino acids
(e.g. Selenomethionine MSE, carboxylated Lysine KCX etc.)?

PROSS turns Selenomethionines (MSE) to Methionines, Carboxlyated Lysines (KCX) to Lysines and Hydroxycesteines (CSO) to Cysteins. Other non native amino acids are recognized and spliced out. This does not affect calculations but mutations at the protein regions near the spliced amino acid (<5A) are less reliable. Consider removing them from sequences that you plan to order.
If you specify position numbers of non native amino acids that are spliced out you will get an error.

Is PROSS good for stabilizing symmetric oligomers?

No and yes. In PROSS you can design only a single chain per query. If your protein is a symmetric dimer with chains A and B for instance, you must select either chain A or B for design. If chain A was selected, chain B will be removed and PROSS "will see" a solvent at the interface region. We therefore recommend to avoid any design of chain A amino acids at the contact site between chains A and B. This can be easily done using the interacting chains option. In general, PROSS works well for monomers and for homo-dimers having a small or reasonably large interface. For instance, it worked well for PTE (PDB entry: 1HZY) that is a homo-dimer. For homo-dimers with huge interfaces or for higher order oligomers PROSS is unlikely to suit.

Is PROSS good for stabilizing antibodies?

Yes, but results are probably less reliable than for other families. Specifically, mutations at CDR regions are not reliable.
If you wish to stabilize an antibody for which there isn't an available crystal structure, you may use our antibody structure-prediction server AbPredict. You are also welcome to contact us for extra guidance as we are interested to show that AbPredict is capable of predicting reliable structure and PROSS on AbPredict models are a nice way to test it.

Is PROSS good for stabilizing membrane proteins?

For modeling PROSS uses a standard energy function designed for soluble proteins. It does not contain any energy terms that take into account the membrane environment and in practice, it is unaware to the membrane and its location.

Is PROSS good for stabilizing small proteins (<100 amino acids)?

PROSS follows a conservative approach in order to minimize false positives. In very small proteins, you might end up with no mutations at all or with a very small number (<4) that is less likely to produce an effect. This is especially true when there are a lot of constraints (small-molecule ligands, interacting chains, specific residues were fixed). We suggest to submit free-of-constraints queries followed by removal of mutations that seem too close to active sites by eye.

How much time takes a PROSS calculation?

The time required for PROSS to complete a calculation depends on the size of your protein and on the number of other queries running in parallel. You may receive the output email within few hours or within 1-2 days. If after 2 days you haven't received the output email please contact us.

Can I submit a PSE file created by PyMOL?

No. You can't submit a PSE file.