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Table 1 The test cases used for Assessment of Pep-3D-Search's performance in mimotope anlysis.

From: Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis

PDB ID

Antibody

Antigen

References

Library size*

Antibody-antigen test cases

1jrh

mAb A6

IFNgammaR

Lang S et al.(2000)

59 × 5

1bj1

rhuMAb VEGF

vascular endothelial growth factor

ChenY et al. (1999)

36 × 6, 3 × 5, 2 × 4

1g9m

mAb 17b

gp120

Enshell-Seijffers D et al. (2003)

10 × 14,1 × 12

1e6j

mAb 13b5

p24

Enshell-Seijffers D et al. (2003)

14 × 14, 2 × 7

1n8z

Herceptin Fab

Her-2

Riemer AB et al. (2004)

5 × 12

1iqd

mAb Bo2C11

Coagulation factor VIII

Villard S et al. (2003)

27 × 12

1yy9

Cetuximab Fab

Epidermal Growth Factor Receptor

Riemer AB et al. (2005)

4 × 10

2adf

82D6A3 IgG

Von Willebrand factor

Vanhoorelbeke K et al. (2003)

2 × 15, 3 × 6

Protein-protein test cases

1avz

Fyn SH3 domain

Nef

Rickles RJ et al. (1994)

8 × 10, 10 × 12

1hx1

Bovine Hsc70

Bag chaperone regulator

Takenaka IM et al. (1995)

8 × 15

  1. *Number of sequences × sequence length.