Fingerprint-based structure retrieval using electron density

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 3, 2011, Pages 1002-1009

  Yin, Shuangye ^a   Dokholyan, Nikolay V ^a  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

Cryo EM; Density fitting; Geometric invariants; Structural genome; Zernike

Indexed keywords

ARTICLE; CRYOELECTRON MICROSCOPY; GENETIC ENGINEERING; GEOMETRY; MATHEMATICAL PARAMETERS; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN STRUCTURE; SCREENING;

CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; INFORMATION STORAGE AND RETRIEVAL; PROTEINS;

EID: 79551486909     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22941     Document Type: Article

References (29)

1. Zhou ZH, Baker ML, Jiang W, Dougherty M, Jakana J, Dong G, Lu G, Chiu W. Electron cryomicroscopy and bioinformatics suggest protein fold models for rice dwarf virus. Nat Struct Mol Biol 2001; 8: 868-873.
2. Chiu W, Baker ML, Jiang W, Zhou ZH. Deriving folds of macromolecular complexes through electron cryomicroscopy and bioinformatics approaches. Curr Opin Struct Biol 2002; 12: 263-269.
3. Ludtke SJ, Chen D-H, Song J-L, Chuang DT, Chiu W. Seeing GroEL at 6 Å resolution by single particle electron cryomicroscopy. Structure 2004; 12: 1129-1136.
4. Ruprecht JJ, Mielke T, Vogel R, Villa C, Schertler GFX. Electron crystallography reveals the structure of metarhodopsin I. EMBO J 2004; 23: 3609-3620.
5. Topf M, Sali A. Combining electron microscopy and comparative protein structure modeling. Curr Opin Struct Biol 2005; 15: 578-585.
6. Baker ML, Jiang W, Wedemeyer WJ, Rixon FJ, Baker D, Chiu W. Ab Initio modeling of the herpesvirus VP26 core domain assessed by cryoEM density. PLoS Comput Biol 2006; 2: e146-e146.
7. Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. Refinement of protein structures by iterative comparative modeling and cryoEM density fitting. J Mol Biol 2006; 357: 1655-1668.
8. Wriggers W, Milligan RA, McCammon JA. Situs: a package for docking crystal structures into low-resolution maps from electron microscopy. J Struct Biol 1999; 125: 185-195.
9. Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ. EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol 2007; 157: 38-46.
10. Canterakis N. 3D Zernike moments and Zernike affine invariants for 3D image analysis and recognition. Proceedings of 11th Scandinavian Conference on Image Analysis, Kangerlussuaq, Greenland, 1999. pp 85-93.
11. Kazhdan M, Funkhouser T, Rusinkiewicz S. Rotation invariant spherical harmonic representation of 3D shape descriptors.Proceedings of the 2003 Eurographics/ACM SIGGRAPH symposium on Geometry processing, Aachen, Germany, 2003. pp 156-164.
12. Novotni M, Klein R. 3D zernike descriptors for content based shape retrieval. Proceedings of the eighth ACM symposium on Solid modeling and applications, Seattle, Washington, USA, 2003. pp 216-225.
13. Yin SY, Proctor EA, Lugovskoy AA, Dokholyan NV. Fast screening of protein surfaces using geometric invariant fingerprints. Proc Natl Acad Sci USA 2009; 106: 16622-16626.
14. Kovacs JA, Wriggers W. Fast rotational matching. Acta Crystallogr Sect D 2002; 58: 1282-1286.
15. Kovacs JA, Chacón P, Cong Y, Metwally E, Wriggers W. Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom. Acta Crystallogr Sect D 2003; 59: 1371-1376.
16. Leibon G, Rockmore DN, Park W, Taintor R, Chirikjian GS. A fast Hermite transform. Theor Comput Sci 2008; 409: 211-228.
17. Sael L, La D, Li B, Rustamov R, Kihara D. Rapid comparison of properties on protein surface. Proteins 2008; 73: 1-10.
18. Sael L, Li B, La D, Fang Y, Ramani K, Rustamov R, Kihara D. Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins 2008; 72: 1259-1273.
19. Venkatraman V, Yang Y, Sael L, Kihara D. Protein-protein docking using region-based 3D Zernike descriptors. BMC Bioinformatics 2009; 10: 407-407.
20. Mak L, Grandison S, Morris RJ. An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison. J Mol Graph Model 2008; 26: 1035-1045.
21. Grandison S, Roberts C, Morris RJ. The application of 3D Zernike moments for the description of "Model-Free" molecular structure, functional motion, and structural reliability. J Comput Biol 2009; 16: 487-500.
22. 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.
23. Zernike F. Inflection theory of the cutting method and its improved form, the phase contrast method. Physica 1934; 1: 689-704.
24. Novotni M, Klein R. Shape retrieval using 3D Zernike descriptors. Computer-Aided Design 2004; 36: 1047-1062.
25. Goddard TD, Huang CC, Ferrin TE. Visualizing density maps with UCSF Chimera. J Struct Biol 2007; 157: 281-287.
26. Tagari M, Newman R, Chagoyen M, Carazo J-M, Henrick K. New electron microscopy database and deposition system. Trends Biochem Sci 2002; 27: 589-589.
27. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000; 28: 235-242.
28. Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005; 33: 2302-2309.
29. The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.