Walls, Peter Hamilton; (1993) Structural aspects of molecular recognition. Doctoral thesis (Ph.D), UCL (University College London).

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Abstract

This thesis describes the design, implementation and application of a novel docking algorithm. Chapter 1 reviews some important facts about proteins and protein structure. Several molecular recognition systems are examined in detail. This Chapter also reviews a representative set of recent protein/protein docking methods and discusses their relative merits. Chapter 2 sets out the aims of the new docking algorithm, called DAPMatch, and gives full details of its implementation on a parallel architecture computer. The testing of the algorithm is also discussed. Subsequent chapters describe the application of the DAPMatch algorithm to a number of docking problems. DAPMatch is used to reconstruct the known structures of three antibody/lysozyme complexes, using the unbound structure of lysozyme. For the first time a model of the D1.3 antibody is used as a target molecule for a docking algorithm. These results are presented in Chapter 3 and analysed in detail to demonstrate their significance; non-native solutions are also examined. Chapter 4 describes the practical use of the DAPMatch algorithm in a modelling situation, to construct a hypothetical structure for the high molecular weight epidermal growth factor complex. Chapter 5 describes the adaptation of the DAPMatch algorithm to investigate α-helix/α-helix docking, and presents the results obtained. Chapter 6 explains the conclusions that were derived from this work, and suggests possible future enhancements to the algorithm.

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