TMBETA-NET: discrimination and prediction of membrane spanning -strands in outer membrane proteins
Authors: Gromiha, M. Michael; Ahmad, Shandar; Suwa, Makiko
Source: Nucleic Acids Research, Volume 33, Supplement 1, 1 July 2005 , pp. W164-W167(4)
Publisher: Oxford University Press
Abstract:We have developed a web-server, TMBETA-NET for discriminating outer membrane proteins and predicting their membrane spanning -strand segments. The amino acid compositions of globular and outer membrane proteins have been systematically analyzed and a statistical method has been proposed for discriminating outer membrane proteins. The prediction of membrane spanning segments is mainly based on feed forward neural network and refined with -strand length. Our program takes the amino acid sequence as input and displays the type of the protein along with membrane-spanning -strand segments as a stretch of highlighted amino acid residues. Further, the probability of residues to be in transmembrane -strand has been provided with a coloring scheme. We observed that outer membrane proteins were discriminated with an accuracy of 89% and their membrane spanning -strand segments at an accuracy of 73% just from amino acid sequence information. The prediction server is available at http://psfs.cbrc.jp/tmbeta-net/.
Document Type: Research Article
Publication date: 2005-07-01
- Nucleic Acids Research (NAR) is a fully Open Access journal, providing rapid publication of leading edge research into the nucleic acids under the following categories: chemistry, computational biology, genomics, molecular biology, nucleic acid enzymes, RNA and structural biology. There is a Survey and Summary section, and methods papers are published
in NAR Methods Online. Each year the first issue is devoted to biological databases, and a later issue to relevant web-based software resources.