PRED-TMR2

Summary

PRED-TMR2 is a new version of PRED-TMR with protein classification capabilities. This software uses a simple artificial neural network which classifies proteins into two classes from their sequences alone: the membrane protein class and the non-membrane protein class. This may be important in the functional assignment and analysis of open reading frames (ORF's) identified in complete genomes and, especially, those ORF's that correspond to proteins with unknown function. The network used here has a simple hierarchical feed-forward topology and a limited number of neurons which makes it very fast. By using only information contained in 11 protein sequences, the method was able to identify, with 100% accuracy, all membrane proteins with reliable topologies collected from several papers in the literature. Applied to a test set of 995 globular, water-soluble proteins, the neural network classified falsely 23 of them in the membrane protein class (97.7% of correct assignment). The method was also applied to the complete SWISS-PROT database with considerable success and on ORF's of several complete genomes.

Availability

PRED-TMR2 is a Web-based tool that can be executed on the Biophysics and Bioinformatics Laboratory of the University of Athens's site.

Related publications

1. Pasquier C, Hamodrakas SJ: An hierarchical artificial neural network system for the classification of transmembrane proteins. Protein engineering 1999, 12:631–4.

2. Pasquier C, Promponas V, Palaios G, Hamodrakas I, Hamodrakas S: PRED-TMR2: An hierarchical neural network to classify proteins as transmembrane and a novel method to predict transmembrane segments. In proceedings of the 21st conference of the Hellenic Society for Biological Sciences. Galissas, Syros island, Greece; 1999.