Expert Antibody Side Chain Placement

Antibody modelling by side chain placement on an homologous backbone conformation is a combinatorially hard problem. This can be made tractable by using a knowledge-based approach in which a heuristic cost function is used to perform a structural search on a database of known structures in order to nd re-usable clusters of side chains. The procedure described yields a plausible structure which would be a good starting point for a detailed molecular dynamics simulation or one which a human expert could manually reene. Declaration I declare that this thesis has been composed by myself and describes my own work. It has not been accepted in any previous application for a degree. Any verbatim extracts have been distinguished by quotation marks and referenced. All sources of information have been speciically acknowledged. Acknowledgements I would like to thank my supervisor Dr. G.J.L. Kemp for the many helpful discussions and his continuous encouragement. I would also like to thank Suzanne Embury for her rapid response to the rare problems with P/FDM, whether real, or more usually, self-innicted. I am also grateful to Prof. J. Fothergill for allowing me to use the computer facilities at Marischal College.