The application of 3D zernike moments for the description of "model-free" molecular structure, functional motion, and structural reliability

Journal of Computational Biology

Volumn 16, Issue 3, 2009, Pages 487-500

  Grandison, Scott ^a   Roberts, Carl ^a,b   Morris, Richard J ^a  

^a JOHN INNES CENTRE   (United Kingdom)

^b UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

Algorithms; Dynamics; Molecular shape; Protein structure; Zernike moments

Indexed keywords

ARTICLE; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; MOLECULE; MOTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; RELIABILITY; SURFACE PROPERTY; THREE DIMENSIONAL IMAGING; UNCERTAINTY;

BINDING SITES; LIGANDS; MODELS, MOLECULAR; MOVEMENT; PROTEINS;

EID: 61749091910     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2008.0083     Document Type: Article

References (55)

1. Agarwal, P.K., Billeter, S.R., Rajagopalan, P.T., et al. 2002. Network of coupled promoting motions in enzyme catalysis. Proc. Natl. Acad. Sci. USA 99, 2794-2799.
2. Berendsen, H.J.C., and Hayward, S. 2000. Collective protein dynamics in relation to function. Curr. Opin. Struct. Biol. 10, 165.
3. Benkovic, S.J., and Hammes-Schiffer, S. 2003. A perspective on enzyme catalysis. Science 301, 1196-1202.
4. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., et al. 1977. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
5. Cai, W., Shao, X., and Maigret, B. 2002. Protein-ligand recognition using spherical harmonic molecular surfaces: towards a fast efficient filter for large virtual throughput screening. J. Mol. Graphics Modelling 20, 313-328.
6. Canterakis, N. 1999. 3D Zernike moments and Zernike affine invariants for 3D image analysis and recognition. 11th Scand. Conf. Image Anal.
7. Celebi, M.E., and Aslandogan, Y.A. 2005. A comparative study of three moment-based shape descriptors. Proc. ITCC'05 1, 788-793.
8. Cruickshank, D.W.J. 1999. Remarks about protein structure precision. Acta Cryst. D55, 583-601.
9. Daniel, R.M., Dunn, R.V., Finney, J.L., et al. 2002. The role of dynamics in enzyme activity. Annu. Rev. Biophys. Biomol. Struct. 32, 69-92.
10. Daras, P., Zarpalas, D., Tzovaras, D., et al. 2005. 3D shape-based techniques for protein classification. IEEE Int. Conf. Image Process. 1257-1260.
11. de Groot, B.L., van Aalten, D.M., Scheek, R.M., et al. 1997. Prediction of protein conformational freedom from distance constraints. Proteins 29, 240-251.
12. DeLano, W.L. 2002. The PyMOL molecular graphics system. Available at: www.pymol.org. Accessed January 5, 2009.
13. Duncan, B.S., and Olson, A.J. 1993a. Approximation and characterization of molecular surfaces. Biopolymers 33, 219-229.
14. Duncan, B.S., and Olson, A.J. 1993b. Shape analysis of molecular surfaces. Biopolymers 33, 231-238.
15. Duncan, B.S., and Olson, A.J. 1995. Approximation and visualization of large-scale motion of protein surfaces. J. Mol. Graphics 13, 250-257.
16. Eisenmesser, E.Z., Bosco, D.A., Akke, M., et al. 2002. Enzyme dynamics during catalysis. Science 295, 1520-1523.
17. Eisenmesser, E.Z., Millet, O., Labeikovsky, W., et al. 2005. Intrinsic dynamics of an enzyme underlies catalysis. Nature 438, 117-121.
18. Frederick, K.K., Marlow, M.S., Valentine, K.G., et al. 2007. Conformational entropy in molecular recognition by proteins. Nature 448, 325-329.
19. Glaser, F., Morris, R.J., Najmanovich, R., et al. 2005. A method for localizing ligand binding pockets in protein structures. Proteins 62, 479-488.
20. Gramada, A., Bourne, P.E. 2006. Multipolar representation of protein structure. BMC Bioinform. 7, 242-255
21. Grandison, S., Penfold, R., and Vanden-Broeck, J.M. 2007. A rapid boundary integral equation technique for protein electrostatics. J. Comp. Phys. 224, 663-680.
22. Grant, J.A., Gallardo, M.A., and Pickup, B.T. 1996. A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape. J. Comp. Chem. 7, 1653-1666.
23. Holm, L., and Sander, C. 1996. Mapping the protein universe. Science 273, 595-603.
24. Jacobs, D.J., Rader, A.J., Kuhn, L.A., et al. 2004. Protein flexibility predictions using graph theory. Proteins 44, 150-165.
25. Kahraman, A., Morris, R.J., Laskowski, R.A., et al. 2007. Shape variation in protein binding pockets and their ligands. J. Mol. Biol. 368, 283-301.
26. Kazhdan, M., Funkhouser, T., and Rusinkiewicz, S. 2003. Rotation invariant spherical harmonic representation of 3D shape descriptors. In Kobbelt, L., Schröder, P., and Hoppe, H., eds. Eurographics Symposium on Geometry Processing. Eurographics Association, Aachen, Germamy, pgs. 156-164.
27. Khersonsky, O., Roodveldt, C., and Tawfik, D.S. 2006. Enzyme promiscuity: evolutionary and mechanistic aspects. Curr. Opin. Chem. Biol. 10, 498-508.
28. Krebs, W.G., Alexandrov, V., Wilson, C.A., et al. 2002. Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic. Proteins 48, 682-695.
29. Krissinel, E., and Henrick, K. 2004. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Cryst. D60, 2256-2268.
30. Lee, R., Razaz, M., and Hayward, S.J. 2003. The DynDom database of protein domain motions. Bioinformatics 19, 1290-1291.
31. Mak, L. 2007. Computational approaches to protein structure and function [Ph.D. dissertation]. John Innes Centre, Norwich, United Kingdom.
32. Mak, L., Grandison, S., and Morris, R.J. 2008. An extension of spherical harmonics to region-based rotationally invariant descriptors for molecular shape description and comparison. J. Mol. Graphics Modelling 26, 1035-1045.
33. Mak, L., and Morris, R.J. 2007. 3D Zernike moments for molecular shape description and comparison, 33-41. In Hochreiter, S., Kueng, J., Palkoska, J., et al., eds. 1st International Conference on Bioinformatics Research and Development (BIRD07), Berlin, Austrian Computer Society.
34. Max, N., and Getzoff, E.D. 1988. Spherical harmonic molecular surfaces. IEEE Comput. Graphics Appl. 8, 42-50.
35. McDonald, I.K., and Thornton, J.M. 1994. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238, 777-793.
36. Morris, R.J., Najmanovich, R.J., Kahraman, A., et al. 2005. Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics 21, 2347-2355.
37. Murshudov, G.N., and Dodson, E.J. 1997. Simplified error estimation a la Cruickshank in macromolecular crystallography. CCP4 Newslett. Protein Crystallogr. 33, 31-39.
38. Najmanovich, R., Kurbatova, N., and Thornton, J. 2008. Detection of 3D atomic similarities and their use in the discrimination of small-molecule protein binding sites. Bioinformatics 24, 105-111.
39. Najmanovich, R.J., Allali-Hassani, A., Morris, R.J., et al. 2007. Analysis of binding site similarity, small molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family. Bioinformatics 23, e104-e109.
40. Novotni, M., and Klein, R. 2004. Shape retrieval using 3D Zernike descriptors. Computer-Aided Design 36, 1047-1062.
41. Pearl, F., Todd, A., Sillitoe, I., et al. 2005. The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res. 33, D247-D251.
42. Ringe D., and Petsko G.A. 1986. Study of protein dynamics by x-ray diffraction. Methods Enzymol. 131, 389-433.
43. Ritchie, D.W., and Kemp, G.J.L. 1999. Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. J. Comp. Chem. 20, 383-395.
44. Sael, L., Li, B., La, D., et al. 2008. Fast protein tertiary structure retrieval based on global surface shape similarity. Proteins 72, 1259-1273.
45. Schneider, T.R. 2000. Objective comparison of protein structures: error-scaled difference distance matrices. Acta Cryst. D56, 714-721.
46. Schneider, T.R. 2002. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta Cryst. D58, 196-298.
47. Sommer, I., Müller, O., Domingues, F.S., et al. 2007. Moment invariants as shape recognition technique for comparing protein binding sites. Bioinformatics 23, 3139-3146.
48. Stec, B., Zhou, R., and Teeter, M.M. 1995. Full-matrix refinement of the protein crambin at 0.83 Å and 130 K. Acta Cryst. D51, 663-681.
49. Thiruv, B., Quon, G., Saldanha, S.A., et al. 2005. Nh3D: a reference dataset of structures of non-homologous proteins. BMC Struct. Biol. 5, 12.
50. Tousignant, A., and Pelletier, J.N. 2004. Protein motions promote catalysis. Chem. Biol. 11, 1037-1042.
51. Wolf-Watz, M., Thai, V., Henzler-Wildman, K., et al. 2004. Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nat. Struct. Mol. Biol. 11, 945-949.
52. Yang, L., Eyal, E., Chennubhotla, C., et al. 2007. Insights into equilibrium dynamics of proteins from comparison of NMR and x-ray data with computational predictions. Structure 15, 741-749.
53. Yang L.W., and Bahar I. 2005. Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. Structure 13, 893-904.
54. Zernike, F. (1934) Diffraction theory of the cut procedure and its improved form, the phase contrast method. Physica 1, 689-704.
55. Zhang, D., and Lu, G. 2004. Review of shape representation and description techniques. Patt. Recogn. 37, 1-19.