Navigating 3D electron microscopy maps with EM-SURFER

BMC Bioinformatics

Volumn 16, Issue 1, 2015, Pages

  Esquivel Rodríguez, Juan ^a   Xiong, Yi ^b   Han, Xusi ^b   Guang, Shuomeng ^b   Christoffer, Charles ^a,b   Kihara, Daisuke ^a,b  

^a Purdue University   (United States)

^b PURDUE UNIVERSITY   (United States)

Author keywords

3D Zernike Descriptors; Database search; Electron density maps; Electron microscopy; EM Data Bank; EMDB; Low resolution structure data; Macromolecular structure; Proteins

Indexed keywords

ELECTRON MICROSCOPES; ELECTRON MICROSCOPY; FUNCTIONS; MACROMOLECULES; PROTEINS; QUERY PROCESSING; SEARCH ENGINES;

DATA BANK; DATABASE SEARCHES; ELECTRON DENSITY MAPS; EMDB; LOW RESOLUTION; MACROMOLECULAR STRUCTURES; ZERNIKE;

ELECTRONS;

PROTEIN;

BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; ELECTRON MICROSCOPY; HUMAN; INTERNET; PROCEDURES; PROTEIN DATABASE; THREE DIMENSIONAL IMAGING;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; IMAGING, THREE-DIMENSIONAL; INTERNET; MICROSCOPY, ELECTRON; MODELS, MOLECULAR; PROTEINS; SOFTWARE;

EID: 84930660890     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0580-6     Document Type: Article

References (25)

1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The protein data bank. Nucleic Acids Res. 2000;28:235-42.
2. Rose PW, Bi C, Bluhm WF, Christie CH, Dimitropoulos D, Dutta S, et al. The RCSB protein data bank: new resources for research and education. Nucleic Acids Res. 2013;41:D475-82.
3. Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, et al. EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res. 2011;39:D456-64.
4. Zhang X, Guo H, Jin L, Czornyj E, Hodes A, Hui WH, et al. A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 A resolution. Elife. 2013;2:e01299.
5. Li X, Mooney P, Zheng S, Booth CR, Braunfeld MB, Gubbens S, et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat Methods. 2013;10:584-90.
6. Liao M, Cao E, Julius D, Cheng Y. Structure of the TRPV1 ion channel determined by electron cryo-microscopy. Nature. 2013;504:107-12.
7. Canterakis N. 3D Zernike Moments and Zernike Affine Invariants for 3D Image Analysis and Recognition. In: 11th Scand. Conf. Image Anal. 1999.
8. Kihara D, Sael L, Chikhi R, Esquivel-Rodríguez J. Molecular surface representation using 3D zernike descriptors for protein shape comparison and docking. Curr Protein Pept Sci. 2011;12:520-30.
9. La D, Esquivel-Rodríguez J, Venkatraman V, Li B, Sael L, Ueng S, et al. 3D-SURFER: software for high-throughput protein surface comparison and analysis. Bioinformatics. 2009;25:2843-4.
10. Li B, Kihara D. Protein docking prediction using predicted protein-protein interface. BMC Bioinformatics. 2012;13:7.
11. Venkatraman V, Yang YD, Sael L, Kihara D. Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinformatics. 2009;10:407.
12. Esquivel-Rodríguez J, Yang YD, Kihara D. Multi-LZerD: multiple protein docking for asymmetric complexes. Proteins. 2012;7:1818-33.
13. Sael L, Kihara D. Detecting local ligand-binding site similarity in non-homologous proteins by surface patch comparison. Proteins. 2012;80:1177-95.
14. Chikhi R, Sael L, Kihara D. Real-time ligand binding pocket database search using local surface descriptors. Proteins. 2010;78:2007-28.
15. Venkatraman V, Chakravarthy PR, Kihara D. Application of 3D Zernike descriptors to shape-based ligand similarity searching. J Cheminform. 2009;1:19.
16. Novotni M, Klein R. 3D zernike descriptors for content based shape retrieval. In: Proc. Eighth ACM Symp. Solid Model. Appl. - SM'03. New York, USA: ACM Press; 2003. p. 216.
17. Sael L, Kihara D. Improved protein surface comparison and application to low-resolution protein structure data. BMC Bioinformatics. 2010;11 Suppl 1:S2.
18. Yin S, Dokholyan NV. Fingerprint-based structure retrieval using electron density. Proteins. 2011;79:1002-9.
19. Funkhouser T, Min P, Kazhdan M, Chen J, Halderman A, Dobkin D, et al. A search engine for 3D models. ACM Trans Graph. 2003;22:83-105.
20. Kazhdan M, Funkhouser T, Rusinkiewicz S. Rotation invariant spherical harmonic representation of 3D shape descriptors. In: Proc. 2003 Eurographics/ACM SIGGRAPH Symp. Geom. Process. Eurographics Association; 2003. 156-164.
21. Xu M, Beck M, Alber F. Template-free detection of macromolecular complexes in cryo electron tomograms. Bioinformatics. 2011;27:i69-76.
22. Sael L, Li B, La D, Fang Y, Ramani K, Rustamov R, et al. Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins. 2008;72:1259-73.
23. Venkatraman V, Sael L, Kihara D. Potential for protein surface shape analysis using spherical harmonics and 3D zernike descriptors. Cell Biochem Biophys. 2009;54:23-32.
24. Sael L, Kihara D. Protein surface representation and comparison: New approaches in structural proteomics. In: Chen JY, Lonardi S, editors. Biol. Data Min. Boca Raton, FL: Chapman & Hall/CRC; 2009. p. 89-109.
25. Carroni M, Kummer E, Oguchi Y, Wendler P, Clare DK, Sinning I, et al. Head-to-tail interactions of the coiled-coil domains regulate ClpB activity and cooperation with Hsp70 in protein disaggregation. Elife. 2014;3:e02481.