Comparative Modeling of Protein Structure—Progress and Prospects

Comparative modeling of protein structure is a process which determines the three-dimensional structure of protein molecules on the basis of amino acid sequence similarity to experimentally linown structures. The procedure is facilitated by the growing database of protein structures obtained from crystallography. In this review a series of stages in the modeling process are identified and discussed. These are: (i) obtaining a reliable amino acid sequence of the structure of interest, (ii) producing a structurally correct sequence alignment, (iii) identifying which structural features are conserved between target and parent structures, (iv) modeling the new pieces of structure, and (v) tests of reliability.