Status of empirical methods for the prediction of protein backbone topography.

Overview

An empirical preduction algorithm which uses information on the shrs on either side) interactions in 20 proteins to assign every residue in a protein to one of five conformational states is described. The conformational states are defined in terms of the backbone dihedral angles of the residue so that the prediction algorithm can be used to generate starting conformations for subsequent energy-minimization procedures, which would be necessary to predict the three-dimensional structure of a protein. An estimate is made of the statistical error in the determination of the parameter- describing the effects of short-range and medium-range interactions in proteins, and it is shown that this statistical error plays a large role in limiting the accuracy of all prediture. Using the method described in this paper, 56% of the residues in 20 proteins were assigned correctly to one of five conformational states. It seems unlikely that any prediction method can significantly improve on this accuracy for assigning residues for specific backbone conformations unless the size of the data base is increased greatly.