Release date 2001
Implementation C++
Authors Pasquier, C., Promponas, V., and Hamodrakas, S.

PRED-CLASS (Pasquier et al. 2001; Promponas et al. 2001) 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.

Pasquier, C., Promponas, V., and Hamodrakas, S. (2001), “PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications.” Proteins: Structure, Function, and Bioinformatics, (Wiley, ed.), 44, 361–9.

Promponas, V., Pasquier, C., and Hamodrakas, S. (2001), “PRED-CLASS: Bioinformatics software for generalized protein classification and genome-wide applications,” in 23rd conference of the hellenic society for biological sciences, Chios island.

Claude Pasquier
Researcher in Computer Science / Computational Biology

Université côte d'Azur, CNRS, I3S Laboratory, Sophia Antipolis