Demo: Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions.

This is a restricted-functionality demo of the methods described in the manuscript "Optimization of therapeutic proteins to delete T-cell epitopes while maintaining beneficial residue interactions" by A.S. Parker, K.E. Griswold, and C. Bailey-Kellogg, CSB 2010. This Demo is for academic use only.

Please refer to the manuscript for a description of the methods and parameters. This web-based demonstration provides limited capabilities: at most a 50-residue peptide from the wild-type protein, 1-4 mutations for the variant, determination of acceptable mutations and coupled residues by family conservation statistics at conservative thresholds, epitope prediction by ProPred at 5% or 10% and evaluation by SMM-align at the most promiscuous threshold, and choices of the weight on the sequence potential alpha at 10%, 50% and 90%. Finally the number of coupled residue pairs is capped at 325, out of a possible (50 choose 2), in order to prevent excessive load on our server. A full-featured Java implementation will be available for download for academic use by contacting Chris Bailey-Kellogg . The Java implementation supports full-length wild-type proteins, more mutations (limited only by computational time), acceptable mutations and coupled residues determined by conservation at any threshold, epitope prediction by ProPred or SMM-align at any threshold, and any continuous choice of alpha (0-1).

Protein name
Wild-type sequence [max 50 amino acids; single-letter codes]
ProPred threshold
Protein family [max 500 entries; "ID\ ALIGNED-SEQUENCE\n"]