HTP: a neural network-based method for predicting the topology of helical transmembrane domains in proteins

In this paper we describe a microcomputer program (HTP) for predicting the location and orientation of alpha-helical transmembrane segments in integral membrane proteins. HTP is a neural network-based tool which gives as output the protein membrane topology based on the statistical propensity of residues to be located in external and internal loops. This method, which uses single protein sequences as input to the network system, correctly predicts the topology of 71 out of 92 membrane proteins of putative membrane orientation, independently of the protein source.