Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.

ABSTRACT:

Background

Prediction of the transmembrane strands and topology of beta-barrel outer membrane proteins is of interest in current bioinformatics research. Several methods have been applied so far for this task, utilizing different algorithmic techniques and a number of freely available predictors exist. The methods can be grossly divided to those based on Hidden Markov Models (HMMs), on Neural Networks (NNs) and on Support Vector Machines (SVMs). In this work, we compare the different available methods for topology prediction of beta-barrel outer membrane proteins. We evaluate their performance on a non-redundant dataset of 20 beta-barrel outer membrane proteins of gram-negative bacteria, with structures known at atomic resolution. Also, we describe, for the first time, an effective

SUBMITTER: Bagos PG 

PROVIDER: S-EPMC545999 | biostudies-literature | 2005 Jan

REPOSITORIES: biostudies-literature