Dynamic combinatorial chemistry utilises reversible reactions to set up a dynamic library of molecules, with the library composition determined by the thermodynamic stability of each library member. Upon addition of a protein template, any library members which bind to the template are stabilised and amplified. Analysis of the library composition enables the identification of molecules which bind to the template protein. The suitability of two enzyme catalysed reactions catalysed by N-acetylneuraminic acid aldolase and subtilisin® Carlsberg was investigated for use in the synthesis of a DCL. A 173 component dynamic combinatorial library was successfully synthesised using these reactions with the resulting library screened against two protein template molecules, wheat germ agglutinin and Div1B. Several methods were investigated for the simplification of DCL analysis including the immobilisation of protein template molecules and the segregation of DCL proteins using semi-permiable membranes, however, the preferred method for the simplification of DCL analysis was found to be the use of size exclusion column chromatography to isolate protein-ligand complexes. This has lead to the identification of novel substrates for wheat germ agglutinin and Div1B.