Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins.
Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops.
This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 Å. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. The backbone of a protein structure favours certain local conformations which include α-helices, β-strands and turns. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution.
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