<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>47</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rezwan Ahmed</style></author><author><style face="normal" font="default" size="100%">Huzefa Rangwala</style></author><author><style face="normal" font="default" size="100%">George Karypis</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">TOPTMH: Topology Predictor for Transmembrane alpha-Helices</style></title><secondary-title><style face="normal" font="default" size="100%">ECML/PKDD (1)</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><pages><style face="normal" font="default" size="100%">23-38</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Alpha-helical transmembrane proteins mediate many key biological processes and represent 20%30% of all genes in many organisms. Due to the difficulties in experimentally determining their high-resolution 3D structure, computational methods to predict the location and orientation of transmembrane helix segments using sequence information are essential. We present, TOPTMH a new transmembrane helix topology prediction method that combines support vector machines, hidden Markov models, and a widely-used rule-based scheme. The contribution of this work is the development of a prediction approach that first uses a binary SVM classifier to predict the helix residues and then it employs a pair of HMM models that incorporate the SVM predictions and hydropathy-based features to identify the entire transmembrane helix segments by capturing the structural characteristics of these proteins. TOPTMH outperforms state-of-the-art prediction methods and achieves the best performance on an independent static benchmark.</style></abstract></record></records></xml>