Bioinformatics III

Graham Kemp > Teaching > Bioinformatics III

Lecture GK-7

Antibodies; MHC-peptide interactions; protein structure databases

Aims

To introduce the structures of some engineered proteins based on antibodies.
To introduce the problem of predicting associations between peptides and class II MHC molecules.
To describe a database of antibody structures, and how this can be used in structure analysis and comparative modelling exercises.

Objectives

After this lecture you will:

be aware of the structures of some engineered proteins based on antibodies, including scFvs and diabodies.
be aware of how bioinformatics techniques can be used in predicting MHC-peptide interactions;
be aware of the utility of a structural database in structure analysis and comparative modelling.

Supplementary Material

Some other creative ways of combining antibody domains to form novel engineered proteins are shown on Nico Mertens' web site.

For more information on modelling class II MHC molecules, see:

Swain, M.T., Brooks, A.J. and Kemp, G.J.L. (2001) An automated approach to modelling class II MHC alleles and predicting peptide binding. Proceedings of the Second IEEE International Symposium on Bio-Informatics and Biomedical Engineering, IEEE Computer Society Press, pp 81-88. (PDF, 328k)

For further information on the antibody database described in the lecture, see:

Kemp, G.J.L., Jiao, Z., Gray, P.M.D. and Fothergill, J.E. (1994) Combining Computation with Database Access in Biomolecular Computing. In Litwin, W. and Risch, T. (eds.), Applications of Databases: Proceedings of the First International Conference, ADB-94, Lecture Notes in Computer Science (vol. 819), Springer-Verlag, Berlin, pp 317-335.

An antibody modelling system that uses the P/FDM antibody database is described in:

Ritchie, D.W. and Kemp, G.J.L. (1997) Using an Object-Oriented Database to Model Antibody Fv Fragments, University of Aberdeen, Technical Report AUCS/TR9702.

This is an extended version of:

Ritchie, D.W. and Kemp, G.J.L. (1997) Modeling Antibody Side Chain Conformations Using Heuristic Database Search. In Gaasterland, T., Karp, P., Karplus, K., Ouzounis, C., Sander, C. and Valencia, A. (eds.) Proceedings of the Fifth International Conference on Intelligent Systems for Molecular Biology, AAAI Press, pp 237-240.