An efficient index-based protein structure database searching method

Zeyar Aung, Wei Fu, Kian Lee Tan

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

22 Scopus citations

Abstract

In this paper, we present a novel indexing method called ProtDex to facilitate fast searching in 3-dimensional protein structure database. In ProtDex, we first build an index on the representative properties of all proteins in the database. When evaluating a query, with the help of the index, we filter out a small candidate list of proteins. Then, we can either directly report them, with their respective rankings, to the user, or do the expensive actual alignments on them upon user's request. Preliminary experimental results show that our solution is up to 16 times faster than the popular DALI method for database searching task (without actual alignments), while its overall accuracy is only slightly inferior to that of DALI. The software is available upon request by sending emails to the authors.

Original languageBritish English
Title of host publicationProceedings - 8th International Conference on Database Systems for Advanced Applications, DASFAA 2003
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages311-318
Number of pages8
ISBN (Electronic)0769518958, 9780769518954
DOIs
StatePublished - 2003
Event8th International Conference on Database Systems for Advanced Applications, DASFAA 2003 - Kyoto, Japan
Duration: 26 Mar 200328 Mar 2003

Publication series

NameProceedings - 8th International Conference on Database Systems for Advanced Applications, DASFAA 2003

Conference

Conference8th International Conference on Database Systems for Advanced Applications, DASFAA 2003
Country/TerritoryJapan
CityKyoto
Period26/03/0328/03/03

Keywords

  • Bioinformatics
  • Biology computing
  • Computer science
  • Databases
  • Drives
  • Genomics
  • Indexes
  • Polymers
  • Proteins
  • Shape

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