Sequence alignment approach to pick up conformationally similar protein fragments

Crystal structure data of globular proteins were used to prepare (phi, psi) probability maps of 20 proteinous amino acids. These maps were compared grid-wise with each other and a conformational similarity index was calculated for each pair of amino acids. A weight matrix, called Conformational Similarity Weight (CSW) matrix, was prepared using the conformational similarity index. This weight matrix was used to align sequences of 21 pairs of proteins whose crystal structures are known. The aligned regions with more than seven contiguous amino acids were further analysed by plotting average weight (W) values of overlapping hepatapeptides in these regions and carrying out curve fitting by Fourier series having TEN harmonics. The protein fragments corresponding to the half-linewidth of peaks were predicted as fragments having similar conformation in the protein pair under consideration. Such an approach allows us to pick up conformationally similar protein fragments with more than 67% accuracy.