Paper Info
Title
MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures.
Abstract
We present a new, first-of-its-kind, fully automated computational tool MOTIF-EM for identifying regions or domains or motifs in cryoEM maps of large macromolecular assemblies (such as chaperonins, viruses, etc.) that remain conformationally conserved. As a by-product, regions in structures that are not conserved are revealed: this can indicate local molecular flexibility related to biological activity. MOTIF-EM takes cryoEM volumetric maps as inputs. The technique used by MOTIF-EM to detect conserved sub-structures is inspired by a recent breakthrough in 2D object recognition. The technique works by constructing rotationally invariant, low-dimensional representations of local regions in the input cryoEM maps. Correspondences are established between the reduced representations ( by comparing them using a simple metric) across the input maps. The correspondences are clustered using hash tables and graph theory is used to retrieve conserved structural domains or motifs. MOTIF-EM has been used to extract conserved domains occurring in large macromolecular assembly maps, including as those of viruses P22 and epsilon 15, Ribosome 70S, GroEL, that remain structurally conserved in different functional states. Our method can also been used to build atomic models for some maps. We also used MOTIF-EM to identify the conserved folds shared among dsDNA bacteriophages HK97, Epsilon 15, and 29, though they have low-sequence similarity. Contact: mitul@cs.stanford.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Year
DOI
Venue
2010
10.1093/bioinformatics/btq195
BIOINFORMATICS
Keywords
DocType
Volume
computational biology,algorithms
Journal
26
Issue
ISSN
Citations 
12
1367-4803
3
PageRank 
References 
Authors
0.67
4
3
Name
Order
Citations
PageRank
Mitul Saha119111.13
Michael Levitt258799.00
Wah Chiu316417.15