Improved methods for template-matching in electron-density maps using spherical harmonics

Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007

Volumn , Issue , 2007, Pages 258-265

  DiMaio, Frank ^a,b   Soni, Ameet ^a,b   Phillips Jr , George N ^a,c   Shavlik, Jude W ^a,b  

^a University of Wisconsin   (United States)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCOMMUNICATIONS; BIOINFORMATICS; CRYSTALLOGRAPHY; HARMONIC ANALYSIS; INFORMATION SCIENCE; MINERALOGY; TEMPLATE MATCHING;

ACCURACY IMPROVEMENT; DENSITY MAPS; FOURIER; HARMONIC DECOMPOSITION; HIGH THROUGHPUTS; IMPROVED METHODS; INTERNATIONAL CONFERENCES; PROTEIN CRYSTALLOGRAPHY; PROTEIN MODELING; RUNNING TIME; SPHERICAL HARMONICS; TEMPLATE MATCHING METHOD; TIME-CONSUMING PROCESSES;

MAPS;

EID: 49049104789     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2007.58     Document Type: Conference Paper

References (18)

1. F. DiMaio, J. Shavlik and G. Phillips (2006). A probabilistic approach to protein backbone tracing in electron-density maps. Proc. ISMB, e81-89.
2. H. Berman and J. Westbrook (2004). The impact of structural genomics on the protein data bank. Am. J. Pharmacogenomics 4(4), 247-52.
3. K. Cowtan (1998). Modified phased translation functions and their application to molecular-fragment location. Acta Cryst. D54, 750-756.
4. A. Kirillov (1994). Representation Theory and Noncommutative Harmonic Analysis. Encyclopaedia of Mathematical Sciences 22. Springer.
5. A. Perrakis, T. Sixma, K. Wilson and V. Lamzin (1997). wARP: Improvement and extension of crystallographic phases. Acta Cryst. D53, 448-55.
6. S. Geman and D. Geman (1984). Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images. IEEE Trans. of PAMI, 721-41.
7. T. Ioerger and J. Sacchettini (2003). The TEXTAL system: Artificial intelligence techniques for automated protein model building. Methods in Enzymology 374, 244-70.
8. T. Ioerger and J. Sacchettini (2002). Automatic modeling of protein backbones in electron density maps via prediction of C-alpha coordinates. Acta Cryst. D58, 2043-54.
9. T. Terwilliger (2003). Automated main-chain model-building by template-matching and iterative fragment extension. Acta Cryst. D59, 38-44.
10. R. Crowther, The Molecular Replacement Method. International Science Reviews Series 13. Gordon and Breach.
11. S. Trapani and J. Navaza (2006). Calculation of spherical harmonics and Wigner d functions by FFT. Acta Cryst. A62.
12. D. Healy, H. Hendriks and P. Kim (1993). Spherical deconvolution with application to geometric quality assurance. Technical Report, Department of Mathematics and Computer Science, Dartmouth College.
13. H. Huang, L. Shen, R. Zhang, F. Makedon, B. Hettleman and J. Pearlman (2005). Surface alignment of 3D spherical-harmonic models: Application to cardiac MRI analysis. Proc. MICCAI 8, 67-74.
14. P. Kostelec and D. Rockmore (2003). FFTs on the rotation group. Working Paper Series, Santa Fe Institute.
15. T. Risbo (1996) Fourier transform summation of Legendre series and D-functions. Journal of Geodesy 70, 383-96.
16. D. Healy, D. Rockmore, P. Kostelec and S. Moore (2003). FFTs for the 2-sphere - improvements and variations. J. Fourier Analysis and Applications 9, 341-85.
17. L. Leherte, J. Glasgow, K. Baxter, E. Steeg and S. Fortier (1997). Analysis of three-dimensional protein images. J. AI research 7, 125-59.
18. J. Greer (1974). Three-dimensional pattern recognition. J. Molecular Biology 82, 279-301.