Linear-time protein 3-D structure searching with insertions and deletions

Tetsuo Shibuya, Jesper Andreas Jansson, Kunihiko Sadakane

Research output: Chapter in book / Conference proceedingConference article published in proceeding or bookAcademic researchpeer-review

1 Citation (Scopus)


It becomes more and more important to search for similar structures from molecular 3-D structure databases in the structural biology of the post genomic era. Two molecules are said to be similar if the RMSD (root mean square deviation) of the two molecules is less than or equal to some given constant bound. In this paper, we consider an important, fundamental problem of finding all the similar substructures from 3-D structure databases of chain molecules (such as proteins), with consideration of indels (i.e., insertions and deletions). The problem has been believed to be very difficult, but its computational difficulty has not been well known. In this paper, we first show that the same problem in arbitrary dimension is NP-hard. Moreover, we also propose a new algorithm that dramatically improves the average-case time complexity for the problem, in case the number of indels k is bounded by some constant. Our algorithm solves the above problem in average O(N) time, while the time complexity of the best known algorithm was O(Nm k + 1), for a query of size m and a database of size N.
Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 9th International Workshop, WABI 2009, Proceedings
Number of pages11
Publication statusPublished - 2 Nov 2009
Externally publishedYes
Event9th International Workshop on Algorithms in Bioinformatics, WABI 2009 - Philadelphia, PA, United States
Duration: 12 Sept 200913 Sept 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5724 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference9th International Workshop on Algorithms in Bioinformatics, WABI 2009
Country/TerritoryUnited States
CityPhiladelphia, PA

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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