Fast automatic particle picking from cryo-electron micrographs using a locally normalized cross-correlation function: a case study - PubMed (original) (raw)

Fast automatic particle picking from cryo-electron micrographs using a locally normalized cross-correlation function: a case study

B K Rath et al. J Struct Biol. 2004 Jan-Feb.

Abstract

Recent progress in single-particle reconstruction methods and cryo-EM techniques has led to the determination of macromolecular structures with unprecedented resolution. The number of particles that goes into the reconstruction is a key determinant in achieving high resolution. Interactive manual picking of particles from an electron micrograph is a very time-consuming, tedious, and inefficient process. We have implemented a fast automatic particle picking procedure in the SPIDER environment. The procedure makes use of template matching schemes and employs a recently developed locally normalized correlation algorithm based on Fourier techniques. As a test, we have used this procedure to pick 70S Escherichia coli ribosomes from a cryo-electron micrograph. Different search strategies including use of a circular mask and asymmetric masks for different orientations of the particle have been explored, and their relative efficiencies are discussed. The results indicate that the procedure can be optimally used to pick ribosomes in a fully automatic way within the limit of selecting less than 10% false positives while missing about 15% of true positives.

PubMed Disclaimer

Cited by

SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.
Shaikh TR, Gao H, Baxter WT, Asturias FJ, Boisset N, Leith A, Frank J. Shaikh TR, et al. Nat Protoc. 2008;3(12):1941-74. doi: 10.1038/nprot.2008.156. Nat Protoc. 2008. PMID: 19180078 Free PMC article.
Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence.
Yang Z, Guo Q, Goto S, Chen Y, Li N, Yan K, Zhang Y, Muto A, Deng H, Himeno H, Lei J, Gao N. Yang Z, et al. Protein Cell. 2014 May;5(5):394-407. doi: 10.1007/s13238-014-0044-1. Epub 2014 Mar 28. Protein Cell. 2014. PMID: 24671761 Free PMC article.
A clarification of the terms used in comparing semi-automated particle selection algorithms in cryo-EM.
Langlois R, Frank J. Langlois R, et al. J Struct Biol. 2011 Sep;175(3):348-52. doi: 10.1016/j.jsb.2011.03.009. Epub 2011 Mar 21. J Struct Biol. 2011. PMID: 21420497 Free PMC article.
The dynamic conformational landscape of gamma-secretase.
Elad N, De Strooper B, Lismont S, Hagen W, Veugelen S, Arimon M, Horré K, Berezovska O, Sachse C, Chávez-Gutiérrez L. Elad N, et al. J Cell Sci. 2015 Feb 1;128(3):589-98. doi: 10.1242/jcs.164384. J Cell Sci. 2015. PMID: 25501811 Free PMC article.
Exploration of parameters in cryo-EM leading to an improved density map of the E. coli ribosome.
LeBarron J, Grassucci RA, Shaikh TR, Baxter WT, Sengupta J, Frank J. LeBarron J, et al. J Struct Biol. 2008 Oct;164(1):24-32. doi: 10.1016/j.jsb.2008.05.007. Epub 2008 Jun 18. J Struct Biol. 2008. PMID: 18606549 Free PMC article.

Fast automatic particle picking from cryo-electron micrographs using a locally normalized cross-correlation function: a case study - PubMed (original) (raw)