Protein secondary structure prediction using sequence profile and conserved domain profile

Seon Kyung Woo, Chang Beom Park, Seong Whan Lee

Research output: Contribution to journalConference articlepeer-review

3 Citations (Scopus)

Abstract

In this paper, we proposed a novel method for protein secondary structure prediction using sequence profile and conserved domain profile. Sequence profile generated from PSI-BLAST (position specific iterated BLAST) has been widely used in protein secondary structure prediction, because PSI-BLAST shows good performance in finding remote homology. Conserved domains kept functional and structural information of related proteins; therefore we could draw remote homology information in conserved domains using RPS-BLAST (reverse position specific BLAST). We combined sequence profile and conserved domain profile to get more remote homology information, and propose a method which used the combined profile to predict the protein secondary structures. In order to verify the effectiveness of our proposed method, we implemented a protein secondary structure prediction system. Overall prediction accuracy reached 75. 9% on the RS126 data set. The improvement by incorporating conserved domain information exceeded 3%, and this result showed that our proposed method could improve significantly the accuracy of protein secondary structure prediction.

Original languageEnglish
Pages (from-to)1-10
Number of pages10
JournalLecture Notes in Computer Science
Volume3645
Issue numberPART II
DOIs
Publication statusPublished - 2005
EventInternational Conference on Intelligent Computing, ICIC 2005 - Hefei, China
Duration: 2005 Aug 232005 Aug 26

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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