Constructing and Evaluating a Comparative Model

A sequence alignment establishes the correspondences between the amino adds in the unknown protein and the template protein (or proteins) from wliich it wiU be built. The three-dimensional structures of two or more related proteins are conveniaitly divided into structurally conserved regions (SCRs) and structurally variable regions (SVRs). The structurally conserved regions correspond to those stretches of maximum sequence identity or secpence 

The simplest type of rigid-body method involves simply transferring the backbone conformation of the core of the protein from a single template to the unknown protein. An alternative is to construct a framework by averaging the structures from a number of protein templates Each template can be given a weight related to its sequence similarity to the unknown target [Srinivasan et al 1996] 

The third method, satisfaction of spatial restraints, adopts a rather different approach to the problem One possible method that would fall into this category would be distance geometry, with the distance constraints being derived from related template structures, 

Loop conformations can be obtained by searching the protein databank for stretches of polypeptide chain that contain the appropriate number of amino acids and also have the correct spatial relationship between the two ends [Jones and Thirup 1986]. A test for amino acid homology may also be included in the criteria for loop selection. This procedure can be made very efficient by precalculating the necessary geometric information from loops in the protein databank and then using screemng methods to identify the loops that can fit. This geometric screen uses information about interatomic distances between key atoms at the base of the loop. Loops that clash with the rest of the protein are rejected. 

The initial structures obtained from a comparative modelling exercise can often be rather high in energy. Energy minimisation is thus often performed to refine the structure, though one should be careful to ensure that the minimisation does not cause any drastic changes and some practitioners deprecate its use. 

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