Structural class prediction: an application of residue distribution along the sequence

Deciphering the native conformation of proteins from their amino acid seque nces is one of the most challenging problems in molecular biology. Informat ion on the secondary structure of a protein can be helpful in understanding its native folded state. In our earlier work on molecular chaperones, we h ave analyzed the hydrophobic and charged patches, short-, medium- and long- range contacts and residue distributions along the sequence. In this articl e, we have made an attempt to predict the structural class of globular and chaperone proteins based on the information obtained from residue distribut ions. This method predicts the structural class with an accuracy of 93 and 96%, respectively, for the four- and three-state models in a training set o f 120 globular proteins, and 90 and 96%, respectively, for a test set of 80 proteins. We have used this information and methodology to predict the str uctural classes of chaperones. Interestingly most of the chaperone proteins are predicted under alpha/beta or mixed folding type. (C) 2000 Elsevier Sc ience B.V. All rights reserved.