ConPred II: A consensus prediction method for obtaining transmembrane topology models with high reliability

Masafumi Arai, Hironori Mitsuke, Masami Ikeda, Jun Xiong Xia, Takashi Kikuchi, Masanobu Satake, Toshio Shimizu

Research output: Contribution to journalArticlepeer-review

181 Citations (Scopus)

Abstract

ConPred II (http://bioinfo.si.hirosaki-u.ac.jp/~ConPred2/) is a server for the prediction of transmembrane (TM) topology [i.e. the number of TM segments (TMSs), TMS positions and N-tail location] based on a consensus approach by combining the results of several proposed methods. The ConPred II system is constructed from ConPredℓite and ConPred_all (previously named ConPred), proposed earlier by our group. The prediction accuracy of ConPredℓite is almost 100%, which is achieved by sacrificing the prediction coverage (20-30%). ConPred_all predicts TM topologies for all the input sequences with accuracies improved by up to 11% over individual proposed methods. In the ConPred II system, the TM topology prediction of input TM protein sequences is executed following a two-step process: (i) input sequences are first run through the ConPredℓite program; (ii) sequences for which ConPredℓite does not give the TM topology are delivered to the ConPred_all program for TM topology prediction. Users can get access to the ConPred II system automatically by submitting sequences to the server. The ConPred II server will return the predicted TM topology models and graphical representations of their contents (hydropathy plots, helical wheel diagrams of predicted TMSs and snake-like diagrams).

Original languageEnglish
Pages (from-to)W390-W393
JournalNucleic acids research
Volume32
Issue numberWEB SERVER ISS.
DOIs
Publication statusPublished - 2004 Jul 1

ASJC Scopus subject areas

  • Genetics

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