PRED-CLASS

Summary

PRED-CLASS is a cascading system of hierarchical, artificial neural networks for the generalized classification of proteins into four distinct classes - transmembrane, fibrous, globular, and mixed - from information solely encoded in their amino acid sequences. The architecture of the individual component networks is kept very simple, reducing the number of free parameters (network synaptic weights) for faster training, improved generalization, and the avoidance of data overfitting. Capturing information from as few as 50 protein sequences spread among the four target classes (6 transmembrane, 10 fibrous, 13 globular, and 17 mixed), PRED-CLASS was able to obtain 371 correct predictions out of a set of 387 proteins (success rate 96%) unambiguously assigned into one of the target classes. The application of PRED-CLASS to several test sets and complete proteomes of several organisms demonstrates that such a method could serve as a valuable tool in the annotation of genomic open reading frames with no functional assignment or as a preliminary step in fold recognition and ab initio structure prediction methods.

Availability

PRED-CLASS is a Web-based tool that can be executed on the Biophysics and Bioinformatics Laboratory of the University of Athens's site.

Related publication

1. Pasquier C, Promponas V, Hamodrakas S: PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications. Proteins 2001, 44:361–9.