title: Fast 3D motif search of EM density maps using a locally normalized cross-correlation function.
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.
authors.affiliation: Wadsworth Center, Empire State Plaza, Albany, NY 12201-0509, USA.
authors.forename: B K
authors.initials: BK
authors.lastname: Rath
authors.forename: R
authors.initials: R
authors.lastname: Hegerl
authors.forename: A
authors.initials: A
authors.lastname: Leith
authors.forename: T R
authors.initials: TR
authors.lastname: Shaikh
authors.forename: T
authors.initials: T
authors.lastname: Wagenknecht
authors.forename: J
authors.initials: J
authors.lastname: Frank
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D020285:Cryoelectron Microscopy / Q000379:methods*; D004583:Electrons; D004926:Escherichia coli / Q000378:metabolism; D015233:Models, Statistical; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry; D019837:Ryanodine Receptor Calcium Release Channel / Q000737:chemistry; D012519:Sarcoplasmic Reticulum / Q000378:metabolism
chemical_list: D019837:Ryanodine Receptor Calcium Release Channel; D012313:RNA