Discovery of protein substructures in EM maps

Keren Lasker, Oranit Dror, Ruth Nussinov, Haim Wolfson

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

Abstract

Cryo-EM has became an increasingly powerful technique for elucidating the structure, dynamics and function of large flexible macromolecule assemblies that cannot be determined at atomic-resolution. A major challenge in analyzing EM maps of complexes is the identification of their subnnits. We propose a fully automated highly efficient method for discovering high-resolution subunits of a complex, given an nu intermediate resolution map, without prior knowledge of their bomuhiries and content. The method extracts helices from an EM map and uses their spatial arrangement to detect candidate subunits. The method was tested successfully on several simulated 8.0Å resolution maps. Tho obtained spatial helix arrangement was sufficient for the discovery of the correct subunits from a dataset of 887 SCOP representativtes.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages423-434
Number of pages12
DOIs
StatePublished - 2005
Event5th International Workshop on Algorithms in Bioinformatics, WABI 2005 - Mallorca, Spain
Duration: 3 Oct 20056 Oct 2005

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3692 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference5th International Workshop on Algorithms in Bioinformatics, WABI 2005
Country/TerritorySpain
CityMallorca
Period3/10/056/10/05

Keywords

  • 3D alignment of secondary structures
  • Intermediate resolution cryo EM maps
  • Macromolecular assemblies
  • Structural bioinformatics

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