Beta-peptide Design Server Documentation

Overview

This application performs fixed-backbone redesigning of beta-3-peptides. Beta-peptides are formed by beta-amino acids, in which the amino groups are attached to the beta carbon instead of the alpha carbon. Therefore beta-peptides have distinct backbone compared to the regular petides. This application search through all 20 beta-amino acids (couterparts of the 20 standard amino acids) and find the best combination that stablize the model. Symmetry-enforced sampling are also available.

Inputs

You need to input

Starting model: The model as a pdb file. Since there is no standard format of the beta-peptide pdb files, the user need to create a rosetta-formatted pdb file. Here is an example.
Repack residues: Residues to be redesigned by Rosetta. Only integers are allow. The numbers should match the numbering used in the input model file. Users can also use format like '13-20; to include all residues between number 11 to 20. If symmetry-based design is used, the user should just input the residues in the first repeat.
Number of repeats [Optional]: For symmetry-based design, the user can input the number of repeating units in the model. This assumes the input model have the format (repeat unit) * n, where n the number of repeats. Therefore only total-symmetry models are currently allowed.
Size of each repeat [Optional]: For symmetry-based design. Must be specified if 'Number of repeats' is given. This tells the server the total number of residues in each repeating unit.
Do not use symmetry in design: Check this box to enforce the server not applying symmetry-constraints, even if the optional parameters is specified. The same reisdues will still be redesigned but the program will not constrain them to have the same amino-acid types and rotamers.

Interpreting Results

The server returns one final model as pdb file. This is the redesigned model. The user can download the examine the model.

Example

To test the server, the user can use the following input, which is the model we used in the following paper. The model can be downloaded here. The following inputs can be used:

Repack residues: 2 5 8 11 14 17 20 23
Number of repeats: 4
Size of each repeat: 24

An example output file can be downloaded here.

Citations

We'd be grateful if you cite our work in publications that make use of the server:

Molski MA, Goodman JL, Chou FC, Baker D, Das R, Schepartz A (2013) Remodeling a beta-peptide bundle. Chemical Science, in press. Link