Potential for protein surface shape analysis using spherical harmonics and 3d zernike descriptors

Cell Biochemistry and Biophysics

Volumn 54, Issue 1-3, 2009, Pages 23-32

  Venkatraman, Vishwesh ^a   Sael, Lee ^b   Kihara, Daisuke ^a,b  

^a PURDUE UNIVERSITY   (United States)

^b Purdue University   (United States)

Author keywords

3D Zernike descriptors; Protein docking prediction; Protein structure comparison; Protein surface; Spherical harmonics

Indexed keywords

PROTEIN;

BINDING SITE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DATABASE; REVIEW; SURFACE PROPERTY;

BINDING SITES; COMPUTER SIMULATION; DATABASES, PROTEIN; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; SURFACE PROPERTIES;

EID: 68549104171     PISSN: 10859195     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12013-009-9051-x     Document Type: Review

References (74)

1. Martin, A. C., Orengo, C. A., Hutchinson, E. G., Jones, S., Karmirantzou, M., Laskowski, R. A., et al. (1998). Protein folds and functions. Structure, 6, 875-884.
2. Thornton, J. M., Todd, A. E., Milburn, D., Borkakoti, N., & Orengo, C. A. (2000). From structure to function: Approaches and limitations. Nature Structural Biology, 7(Suppl), 991-994.
3. Kihara, D., & Skolnick, J. (2004). Microbial Genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q. Proteins, 55, 464-473.
4. Mizuguchi, K., & Go, N. (1995). Seeking significance in three-dimensional protein structure comparisons. Current Opinion in Structural Biology, 5, 377-382.
5. Kihara, D., & Skolnick, J. (2003). The PDB is a covering set of small protein structures. Journal of Molecular Biology, 334, 793-802.
6. Shindyalov, I. N., & Bourne, P. E. (1998). Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering, 11, 739-747.
7. Holm, L., & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. Journal of Molecular Biology, 233, 123-138.
8. Mizuguchi, K., & Go, N. (1995). Comparison of spatial arrangements of secondary structural elements in proteins. Protein Engineering, 8, 353-362.
9. Betancourt, M. R., & Skolnick, J. (2004). Local propensities and statistical potentials of backbone dihedral angles in proteins. Journal of Molecular Biology, 342, 635-649.
10. Kinoshita, K., & Nakamura, H. (2003). Identification of protein biochemical functions by similarity search using the molecular surface database eF-site. Protein Science, 12, 1589-1595.
11. Taylor, W. R., & Orengo, C. A. (1989). Protein structure alignment. Journal of Molecular Biology, 208, 1-22.
12. Lozano, M., & Escolano, F. (2006). Protein classification by matching and clustering surface graphs. Pattern Recognition, 39(4), 539-551.
13. Rogen, P., & Fain, B. (2003). Automatic classification of protein structure by using Gauss integrals. Proceedings of the National Academy of Sciences of the United States of America, 100, 119-124.
14. Pan, T., & Uhlenbeck, O. C. (1993). Circularly permuted DNA, RNA and proteins-A review. Gene, 125, 111-114.
15. Kolodny, R., Petrey, D., & Honig, B. (2006). Protein structure comparison: Implications for the nature of 'fold space', and structure and function prediction. Current Opinion in Structural Biology, 16, 393-398.
16. Burley, S. K. (2000). An overview of structural genomics. Nature Structural Biology, 7(Suppl), 932-934.
17. Todd, A. E., Marsden, R. L., Thornton, J. M., & Orengo, C. A. (2005). Progress of structural genomics initiatives: An analysis of solved target structures. Journal of Molecular Biology, 348, 1235-1260.
18. Westbrook, J., Feng, Z., Chen, L., Yang, H., & Berman, H. M. (2003). The Protein Data Bank and structural genomics. Nucleic Acids Research, 31, 489-491.
19. Yokoyama, S., Matsuo, Y., Hirota, H., Kigawa, T., Shirouzu, M., Kuroda, Y., et al. (2000). Structural genomics projects in Japan. Progress in Biophysics and Molecular Biology, 73, 363-376.
20. Todd, A. E., Orengo, C. A., & Thornton, J. M. (2001). Evolution of function in protein superfamilies from a structural perspective. Journal of Molecular Biology, 307, 1113-1143.
21. Redfern, O. C., Dessailly, B., & Orengo, C. A. (2008). Exploring the structure and function paradigm. Current Opinion in Structural Biology, 18, 394-402.
22. Hawkins, T., & Kihara, D. (2007). Function prediction of uncharacterized proteins. Journal of Bioinformatics and Computational Biology, 5, 1-30.
23. Sael, L., & Kihara, D. (2009). Protein surface representation and comparison: New approaches in structural proteomics. In J. Chen & S. Lonardi (Eds.), Biological data mining. Boca Raton, FL, USA: Chapman & Hall/CRC Press.
24. Via, A., Ferre, F., Brannetti, B., & Helmer-Citterich, M. (2000). Protein surface similarities: A survey of methods to describe and compare protein surfaces. Cellular and Molecular Life Sciences, 57, 1970-1977.
25. Exner, T. E., Keil, M., & Brickmann, J. (2002). Pattern recognition strategies for molecular surfaces. I. Pattern generation using fuzzy set theory. Journal of Computational Chemistry, 23, 1176-1187.
26. Sael, L., Li, B., La, D., Fang, Y., Ramani, K., Rustamov, R., et al. (2008). Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins, 72, 1259-1273.
27. Albou, L. P., Schwarz, B., Poch, O., Wurtz, J. M., & Moras, D. (2008). Defining and characterizing protein surface using alpha shapes. Proteins, 76, 1-12.
28. Bock, M. E., Cortelazzo, G. M., Ferrari, C., & Guerra, C. (2005). Identifying similar surface patches on proteins using a spin-image surface representation. pp. 417-428.
29. Ankerst, M., Kastenmuller, G., Kriegel, H.-P., & Seidl, T. (1999). 3D shape histograms for similarity search and classification in spatial databases. pp. 207-226.
30. Hu, M. (1962). Visual pattern recognition by moment invariants. IRE Transactions on Information Theory, 8, 179-187.
31. Teague, M. (1980). Image analysis via the general theory of moments. Journal of the Optical Society of America, 70, 920-930.
32. Teh, C. H., & Chin, R. T. (1988). On image-analysis by the methods of moments. IEEE Transactions on Pattern Analysis and Machine Intelligence, 10, 496-513.
33. Biedenham, L., & Louck, J. (1981). Angular momentum in quantum physics. Reading, MA, USA: Addison-Wesley.
34. Lisle, I., & Huang, S. (2007). Algorithms for spherical harmonic lighting. In: GRAPHITE'07: Proceedings of the 5th international conference on Computer graphics and interactive techniques in Australia and Southeast Asia, New York, NY, USA, ACM (pp. 235-238).
35. Max, N., & Getzoff, E. (1988). Spherical harmonic molecular surfaces. IEEE Computer Graphics and Applications, 8(4), 42-50.
36. Kovacs, J. A., & Wriggers, W. (2002). Fast rotational matching. Acta Crystallographica. Section D, Biological Crystallography, 58, 1282-1286.
37. Funkhouser, T., Min, P., Kazhdan, M., Chen, J., Halderman, A., Dobkin, D., et al. (2003). A search engine for 3D models. ACM Transactions on Graphics, 22, 83-105.
38. Morris, R. J., Najmanovich, R. J., Kahraman, A., & Thornton, J. M. (2005). Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics, 21, 2347-2355.
39. Kazhdan, M., Funkhouser, T., & Rusinkiewicz, S. (2003). Rotation invariant spherical harmonic representation of 3D shape descriptors. In Proceedings of the 2003 Eurographics/ACM SIGGRAPH symposium on geometry processing, vol 43 (pp. 156-164).
40. Edmonds, A. R. (1957). Angular momentum in quantum mechanics. Princeton, NJ: Princeton University Press.
41. Mak, L., Grandison, S., & Morris, R. J. (2007). An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison. Journal of Molecular Graphics & Modelling, 26, 1035-1045.
42. Zhang, D., & Lu, G. (2004). Review of shape representation and description techniques. Pattern Recognition, 37(1), 1-19.
43. Canterakis, N. (1999). 3D Zernike moments and Zernike affine invariants for 3D image analysis and recognition. In: Proc. 11th scandinavian conference on image analysis (pp. 85-93).
44. Novotni, M., & Klein, R. (2003). 3D Zernike descriptors for content based shape retrieval. In: ACM symposium on solid and physical modeling, proceedings of the eighth ACM symposium on Solid modeling and applications (pp. 216-225).
45. Sael, L., La, D., Li, B., Rustamov, R., & Kihara, D. (2008). Rapid comparison of properties on protein surface. Proteins, 73, 1-10.
46. Venkatraman, V., Yang, Y. D., Sael, L., & Kihara, D. (2009). Protein-protein docking using region-based 3D Zernike descriptors (submitted).
47. Connolly, M. L. (1983). Solvent-accessible surfaces of proteins and nucleic acids. Science, 221, 709-713.
48. Gramada, A., & Bourne, P. E. (2006). Multipolar representation of protein structure. BMC. Bioinformatics, 7, 242.
49. Zhang, T., Chen, W., Hu, M., & Peng, Q. (2005). A similarity computing algorithm for proteins. In Ninth international conference on computer aided design and computer graphics (CAD-CG'05) (pp. 168-172).
50. Binkowski, T. A., & Joachimiak, A. (2008). Protein functional surfaces: Global shape matching and local spatial alignments of ligand binding sites. BMC Structural Biology, 8, 45.
51. Zhang, Z., & Grigorov, M. G. (2006). Similarity networks of protein binding sites. Proteins, 62, 470-478.
52. Kihara, D., Sael, L., & Chikhi, R. (2009). Local surface shape-based protein function prediction using Zernike descriptors. Biophysical Journal, 96, 650a.
53. Chikhi, R., & Kihara, D. (2009). Real-time protein binding ligand prediction using local surface descriptors (submitted).
54. Liang, J., Edelsbrunner, H., & Woodward, C. (1998). Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science, 7, 1884-1897.
55. Kinoshita, K., & Nakamura, H. (2005). Identification of the ligand binding sites on the molecular surface of proteins. Protein Science, 14, 711-718.
56. Kalidas, Y., & Chandra, N. (2008). PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins. Journal of Structural Biology, 161, 31-42.
57. Kahraman, A., Morris, R. J., Laskowski, R. A., & Thornton, J. M. (2007). Shape variation in protein binding pockets and their ligands. Journal of Molecular Biology, 368, 283-301.
58. Ritchie, D. W. (2008). Recent progress and future directions in protein-protein docking. Current Protein & Peptide Science, 9, 1-15.
59. Chen, R., Li, L., & Weng, Z. (2003). ZDOCK: An initial-stage protein-docking algorithm. Proteins, 52, 80-87.
60. Ritchie, D. W., & Kemp, G. J. (2000). Protein docking using spherical polar Fourier correlations. Proteins, 39, 178-194.
61. Mendez, R., Leplae, R., De, M. L., & Wodak, S. J. (2003). Assessment of blind predictions of protein-protein interactions: Current status of docking methods. Proteins, 52, 51-67.
62. Ritchie, D. W. (2003). Evaluation of protein docking predictions using Hex 3. 1 in CAPRI rounds 1 and 2. Proteins, 52, 98-106.
63. Mavridis, L., Hudson, B. D., & Ritchie, D. W. (2007). Toward high throughput 3D virtual screening using spherical harmonic surface representations. Journal of Chemical Information and Modeling, 47, 1787-1796.
64. Ritchie, D. W., & Kemp G. J. L. (1999). Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. Journal of Computational Chemistry, 20(4), 383-395.
65. Grant, J., Gallardo, M., & Pickup, B. (1998). A fast method of molecular shape comparison. A simple application of a Gaussian description of molecular shape. pp. 1653-1666.
66. Cai, W., Xu, J., Shao, X., Leroux, V., Beautrait, A., & Maigret, B. (2008). SHEF: A vHTS geometrical filter using coefficients of spherical harmonic molecular surfaces. Journal of Molecular Modeling, 14, 393-401.
67. McGann, M. R., Almond, H. R., Nicholls, A., Grant, J. A., & Brown, F. K. (2003). Gaussian docking functions. Biopolymers, 68, 76-90.
68. Daras, D., Zarpalas, D., Tzovaras, D., & Strintzis, M. G. (2005). 3D shape-based techniques for protein classification. In: International conference on image processing (pp. 1130-1133).
69. Sael, L., & Kihara, D. (2008). Protein local surface shape comparison. Unpublished data.
70. Lawrence, M. C., & Colman, P. M. (1993). Shape complementarity at protein/protein interfaces. Journal of Molecular Biology, 234, 946-950.
71. Mitchell, J. C., Kerr, R., & Ten Eyck, L. F. (2001). Rapid atomic density methods for molecular shape characterization. Journal of Molecular Graphics & Modelling, 19, 325-390.
72. Wolfson, H., & Rigoutsos, I. (1997). Geometric hashing: An overview. Computing in Science and Engineering, 4(4), 10-21.
73. Mintseris, J., Wiehe, K., Pierce, B., Anderson, R., Chen, R., Janin, J., et al. (2005). Protein-protein docking benchmark 2. 0: An update. Proteins, 60, 214-216.
74. Chen, R., & Weng, Z. (2003). A novel shape complementarity scoring function for protein-protein docking. Proteins, 51, 397-408.