Epitome

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Text from the NAR 2007 Database Issue (Database Summaries) by permission of Oxford University Press.

Epitome is NAR Database No. 813.

Contents

Database Description

Epitome is a database of all known antigenic residues and the antibodies that interact with them, including a detailed description of the residues involved in the interaction and their sequence/structure environments. Each entry in the database describes one interaction between a residue on an antigenic protein and a residue on an antibody chain. Every interaction is described using the following parameters: (*1) PDB identifier, (*2) antigen chain ID (*3) PDB position of the antigenic residue, (*4) type of antigenic residue and its sequence environment, (*5) antigen residue secondary structure state, (*6) antigen residue solvent accessibility, (*7) antibody chain ID, (*8) type of antibody chain (heavy or light), (*9) CDR number, (*10) PDB position of the antibody residue, and (*11) type of antibody residue and its sequence environment. Additionally, interactions can be visualized using an interface to Jmol. The database is available at http://www.rostlab.org/services/epitome/.

Acknowledgements

This work was supported by the grants RO1-GM64633-01 from the National Institutes of Health (NIH), and RO1-LM07329-01 from the National Library of Medicine (NLM).

References

  1. Schlessinger A., Ofran Y., Yachdav G., Rost B. (2006) Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res. Vol. 34, Database issue

Authors

Schlessinger A.1,2,3, Ofran Y.1,2, Yachdav G.1,2,3 and Rost B.1,2,3

1CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St Nicholas Avenue room 804, New York, NY 10032, USA
2Columbia University Center for Computational Biology and Bioinformatics (C2B2), 1130 St Nicholas Avenue, room 804, New York, NY 10032, USA
3NorthEast Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St. Nicholas Avenue room 804, New York, NY 10032, USA


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