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Table 1 SakSTAR 71-87 Peptide.

From: Optimization algorithms for functional deimmunization of therapeutic proteins

Variant

SakSTAR 71-87

E

B

C

ΔΔG°

S

wild type

TAYKEFRVVELDPSAKI

16

0

0.00

0.00

9

1 substitution

Warmerdam

......A..........

12

1

0.75

0.43

7

BLOSUM

........T........

8

0

-0.74

1.13

5

Conservation

........D........

5

1

0.72

1.90

3

FoldX

........K........

9

1

0.94

0.00

5

2 substitutions

Warmerdam

......A..A.......

15

2

2.48

1.00

11

BLOSUM

........T.F......

5

0

0.28

3.12

2

Conservation

.....K..D........

1

2

0.51

4.14

1

FoldX

........K....T...

5

1

2.43

0.18

6

3 substitutions

Warmerdam

......A..A.A.....

20

3

4.96

0.22

14

BLOSUM

...E....T.F......

3

0

0.45

3.73

1

Conservation

...D.K..D........

0

3

1.46

4.52

0

FoldX

...A....K....T...

3

2

3.44

0.08

4

4 substitutions

Warmerdam

...Q..S..S....S..

15

2

4.37

2.12

7

BLOSUM

......QMA.F......

1

0

3.91

4.66

2

Conservation

n/a

     

FoldX

...AD...K....T...

2

2

1.50

-0.30

4

  1. Variants of SakSTAR 71-87 by Warmerdam et al. B1919, as well as by our dynamic programming algorithm, optimizing for ProPred and allowing mutations according to BLOSUM, conservation, or FoldX. E: number of ProPred epitopes; B, C, and ΔΔG°: total substitution penalty under BLOSUM, conservation, and FoldX, resp.; S: number of SMM-align epitopes.
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BMC Bioinformatics

ISSN: 1471-2105

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