J Struct Biol. 2003 Oct-Nov;144(1-2):95-103.

Fast 3D motif search of EM density maps using a locally normalized cross-correlation function.

Rath BK, Hegerl R, Leith A, Shaikh TR, Wagenknecht T, Frank J.

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Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA.

Abstract

Three-dimensional motif search is becoming increasingly important both in the search for molecular signatures within a tomographic reconstruction, at low resolution, and in the search for atomic structures within high-resolution cryo-EM maps of macromolecular complexes. The present work describes the implementation of a fast local correlation algorithm suitable for template matching in the SPIDER environment. Two examples are given, one in each of the areas of application: (i). within a 7.8A single-particle reconstruction of the Escherichia coli ribosome, four proteins and one RNA structure were located with high accuracy; (ii). within a cryo-tomogram of sarcoplasmic reticulum vesicles, ryanodine receptors were located in positions that agreed with expert knowledge.

PMID:: 14643212; [PubMed - indexed for MEDLINE]

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