Nanobody structures

Abstract

Many strategies have been developed to predict the function of amino acids and the effects of mutations. A multiple sequence alignment for a protein superfamily can be a powerful tool to transfer such information, but it also contains other relevant information about sequence variation and correlated mutations, for example. 3DM is a molecular-class-specific information system that creates an accurate structure-based multiple sequence alignment. Many derived data, such as correlated mutations, sequence variation, homology models, automatic mutation analyses, etc. are included. All of the information is stored in a relational database that revolves around a comprehensive 3D numbering scheme that encompasses all structurally equivalent positions, which allows the linking of all available data and the transfer of information between all sequences and structures. When building the 3DM for VHHs it was decided to not include the CDRs because their alignment is not reliably possible in an automated version. Consequently, homology models weren’t constructed and CDRs were not included in the alignments, correlated mutation calculations, but these topics are discussed in other chapters of this thesis.