welcome. Rosetta design can be used to identify sequences compatible with a given protein backbone. Some of Rosetta design's successes include the design of a novel protein fold, redesign of an existing protein for greater stability, increased binding affinity between two proteins, and the design of novel enzymes.

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

Rosetta Protein Design. The Increase Affinity protocol is based on the premise that increasing buried hydrophobic surface area and/or decreasing buried hydrophilic surface area will generally lead to enhanced binding affinity provided steric clashes are not introduced and buried polar groups are not left without a hydrogen bond partner.

CSV input instructions. To use the "comma separated value" (CSV) format simply pasted your comma-delimited data in the textbox. The input text must take the same form as the manual input table (22 rows, the first being the residue positions, the next 20 being the amino acids in alphabetical order by one-letter code, the last being the stop penalty for that position).

This file specifies which residues will be varied during the design run. Below is an example resfile which performs design at a subset of positions and repacking everywhere else.

The purpose of Scaffold Select is to help identify proteins that would make good scaffolds for the design of epitope-binding proteins. The protocol performs searches through a protein-peptide database looking for peptides which have high sequence similarity to the target epitope.

Please fill out the form below to submit a design job. Note: This server will design at most 200 positions. If your PDB file contains more than 200 residues, you must upload a resfile (see resfile format) which specifies which residues you want to design.For the full resfile format specification, see the Rosetta release manual.

Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins ...

Rosetta Commons Developers Participation Agreement ...

Rosetta Protein Design. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.