SwiftLib degenerate codon library optimizer
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
Rosetta.design3.5computational protein design software
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.
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crystal structure of Top7
Comparison of the computationally designed model (blue) to the solved x-ray structure (red) of Top7 reveals a backbone RMSD of only 1.17A.