Protein bağlanma bölgesi ve protein yüzeyi yapısal hizalanması aracı prototipi iMatch'in performans ve doğruluk analizi

Protein structure alignment is the task of finding an optimal transformation between two protein structures that minimizes the distances between two molecules. Since 3D protein structure is one of the most important characteristics of proteins and the number of deposited structures in the Protein Data Bank (PDB) is exponentially increasing, the structural alignment of proteins has been studied extensively. The structural alignment of proteins can provide evolutionary information, allow prediction of function, identify homologs and provide a classification mechanism. In this thesis, a new structural alignment method called iMatch has been proposed. iMatch is based on the pairwise structural alignment component of MultiProt and is designed as the structural alignment component for alignment of binding sites onto protein surfaces. iMatch uses the object recognition method geometric hashing to identify the similar local regions on the proteins. These local regions are then clustered according to their transformation similarities and extended further to obtain a final global alignment. The heuristics used throughout the alignment process and the working mechanism of iMatch has been explained in detail. iMatch is a highly customizable alignment method due to its parametric nature. This flexibility allows the configuration of iMatch according to the task in hand for better accuracy. Furthermore, this parametric nature grants iMatch the ability to be adjusted for the binding site – surface alignment. The default optimal parameters have been identified by a two-step optimization process and each parameter's effect to the alignment speed and accuracy has been inspected thoroughly for future studies on binding site – surface alignment. The overall performance of iMatch has been evaluated on three different well-known datasets against state-of-the-art structural alignment methods existing today.