De-immunization results for mutation loads of <i>k</i> = 1,2,3.

<p>De-immunization results for mutation loads of <i>k</i> = 1,2,3.</p

Population-specific design of de-immunized protein biotherapeutics - Fig 5

<p>(A) Correlation of experimental and predicted immunogenicity of each peptide. The experimental immunogenicity score of a peptide is defined as the linear combination of the individual experimentally determined relative HLA binding affinity of each HLA allele h ∈ H weighted by the HLA allele frequency. (B) Correlation of experimental and predicted immunogenicity of the whole redesigned region. The summarized immunogenicity score of the whole region is the linear combination of the overlapping peptides used to reconstruct the region, normalized by total number of peptides used. The predicted immunogenicity scores per peptide were computed according to our immunogenicity objective function. The red lines are a fitted linear regression and the red tubes represent their 95-confidence interval.</p

Depiction of the parallel two-phase rectangle splitting approach.

<p>(A) First, the boundaries of the Pareto front are identified. (B) Then, the space between the boundaries is evenly divided and searched in parallel for nondominated points using the ε-constraint method. (C) The identified nondominated points are used to initiate rectangle search spaces which can be processed in parallel using the standard rectangle-splitting approach, by splitting the rectangle in half and searching independently the bottom and top half (D). If the corner points of the rectangles are found during the search, it is proofs, that no further nondominated point resides within the search space and all points have been identified.</p

Evolutionary couplings-based model and FoldX prediction correlations.

<p>The red line is a fitted linear regression, and the red tube represents its 95-confidence interval. The orange-circled dots are the two mutational designs with the highest discrepancy. FoldX predicted these two mutations less deleterious compared maximum entropy model, although both designs introduced a mutation at a membrane-binding site.</p

Bi-objective integer linear program formulation of the de-immunization problem.

<p>Bi-objective integer linear program formulation of the de-immunization problem.</p