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Open Access Highly Accessed Research article

Antibody-protein interactions: benchmark datasets and prediction tools evaluation

Julia V Ponomarenko12* and Philip E Bourne12

Author Affiliations

1 San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA

2 Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA

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BMC Structural Biology 2007, 7:64  doi:10.1186/1472-6807-7-64

Published: 2 October 2007

Additional files

Additional file 1:

The representative structures of protein antigens (numbered) and antibody-protein complexes represented different epitopes for each antigen (epitopes inferred from one-chain antibody fragments are in italic). The data provides curated information on 82 3D structures of antibody-protein complexes (dataset #1) represented 169 structures of antibody-protein complexes available in the PDB of January, 2006 and used in this work.

Format: DOC Size: 303KB Download file

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Additional file 2:

The detailed statistics on the prediction results for 59 representative epitope. This table provides additional information that complements the Tables 2 and 3. The analysis was performed using 59 representative epitopes from dataset #2 that were inferred from structures of one-chain (monomer) antigens in complexes with two-chain antibody fragments.

Format: XLS Size: 140KB Download file

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