Selection and Superimposition of Binding Sites

A somewhat more elaborate scheme was proposed by Matter and Schwab [4]. Starting from a global 3D alignment, in an iterative procedure they focus on those amino acids which, after superimposition, show a low RMS deviation. Only these residues are considered in the next round of structure alignment. In this way they arrive at an unbiased superimposition of a large number of proteins focusing on the most conserved parts of the structure. 

However, in many cases the proteins considered in the analysis are very similar and show only little structural variation. In these cases a superimposition of structurally conserved regions with standard protein homology modeling tools has yielded satisfactory protein superimpositions suited for the GRID/PCA or GRID/ GPGA analysis [8,9,13,17]. 

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