Demo: functional deimmunization of therapeutic proteins

This is a restricted-functionality demo of the methods described in the paper "Optimization algorithms for functional deimmunization of therapeutic proteins" by A.S. Parker, W. Zheng, K.E. Griswold, and C. Bailey-Kellogg, BMC Bioinformatics 2010, 11:180.

Please refer to the paper 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 by BLOSUM-62, and epitope prediction by ProPred matrices at a 5% or 10% threshold. A full-featured Java implementation is freely available 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 determined by BLOSUM, conservation, or Fold-X, and epitope prediction by ProPred or SMM-align.

Wild-type sequence [max 50 amino acids; single-letter codes]
ProPred threshold