PROTEINS POCKETS ANALYSIS AND DESCRIPTION

Virginio Cantoni, Riccardo Gatti, Luca Lombardi

Abstract

The development of computational techniques to guide the experimental processes is an important step for the determination of the protein functions. The purpose of the activity here described is the characterization of the active sites in protein surfaces and their quantitative representation. A few pocket parameters like volume, travel depth, mouth area and perimeter, amplitude parameters, interfacial area ratio, summit density and mean summit curvature are hierarchically accessible through a concavity tree that topologically represents the entire protein molecule. This structural representation is particularly useful for the evaluation of binding pockets, the comparison of the morphological similarity and the identification of potential ligand docking.

References

  1. Arcelli, C. and Sanniti Di Baja, G. (1978). Polygonal covering and concavity tree of binary digital pictures. In Proceeding International Conference MECO 78, page 292297.
  2. Barber, C. B. and Dobkin, D. P. (1996). The quickhull algorithm for convex hulls. ACM Transactions on Mathematical Software, 22:469-483.
  3. Binkowski, A. T., Naghibzadeh, S., and Liang, J. (2003). Castp: Computed atlas of surface topography of proteins. Nucl. Acids Res., 31(13):3352-3355.
  4. Blunt, L. and Jiang, X. (2003). Advanced Techniques for Assessment Surface Topography (1st edn.). Penton Press, London.
  5. Borgefors, G. and Sanniti Di Baja, G. (1992). Methods for hierarchical analysis of concavities. In Proceedings of the Conference on Pattern Recognition (ICPR), volume 3, pages 171-175.
  6. Borgefors, G. and Sanniti Di Baja, G. (1996). Analyzing non convex 2d and 3d patterns. Computer Vision and Image Understanding, 63(1):145-157.
  7. Brady, G. P. and Stouten, P. F. (2000). Fast prediction and visualization of protein binding pockets with pass. J Comput Aided Mol Des, 14(4):383-401.
  8. Cantoni, V., Gatti, R., and Lombardi, L. (2009a). Approaches for protein surface curvature analysis. In ICIAP 2009, in press.
  9. Cantoni, V., Gatti, R., and Lombardi, L. (2009b). Proteins pockets quantitative description. In DIS-UNIPV internal report.
  10. Cantoni, V., Gatti, R., and Lombardi, L. (2009c). Segmentation of ses for protein structure analysis. In BIOINFORMATICS 2010, submitted to.
  11. Coleman, R. G., Burr, M. A., Souvaine, D. L., and Cheng, A. C. (2005). An intuitive approach to measuring protein surface curvature. Proteins, 61(4):1068-1074.
  12. Coleman, R. G. and Sharp, K. A. (2006). Travel depth, a new shape descriptor for macromolecules: application to ligand binding. J Mol Biol, 362(3):441-458.
  13. Giard, J., Patrice, R. A., and Macq, B. (2008). Fast and accurate travel depth estimation for protein active site prediction. SPIE Electronic Imaging, San Jose 2008, pages 0Q-10Q.
  14. Glaser, F., Morris, R. J., Najmanovich, R. J., Laskowski, R. A., and Thornton, J. M. (2006). A method for localizing ligand binding pockets in protein structures. Proteins, 62(2):479-488.
  15. Glaser, F., Rosenberg, Y., Kessel, A., Pupko, T., and BenTal, N. (2005). The consurf-hssp database: the mapping of evolutionary conservation among homologs onto pdb structures. Proteins, 58(3):610-617.
  16. Huang, B. and Schroeder, M. (2006). Ligsitecsc: predicting ligand binding sites using the connolly surface and degree of conservation. BMC Structural Biology, 6(1):19+.
  17. Laskowski, R. A. (1995). Surfnet: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph, 13(5).
  18. Laskowski, R. A., Luscombe, N. M., Swindells, M. B., and Thornton, J. M. (1996). Protein clefts in molecular recognition and function. Protein Sci, 5(12):2438- 2452.
  19. Levitt, D. G. and Banaszak, L. J. (1992). Pocket: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph, 10(4):229-234.
  20. Liang, J., Edelsbrunner, H., and Woodward, C. (1998). Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci, 7(9):1884-1897.
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Paper Citation


in Harvard Style

Cantoni V., Gatti R. and Lombardi L. (2010). PROTEINS POCKETS ANALYSIS AND DESCRIPTION . In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 211-216. DOI: 10.5220/0002725302110216


in Bibtex Style

@conference{bioinformatics10,
author={Virginio Cantoni and Riccardo Gatti and Luca Lombardi},
title={PROTEINS POCKETS ANALYSIS AND DESCRIPTION},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={211-216},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002725302110216},
isbn={978-989-674-019-1},
}


in EndNote Style

TY - CONF
JO - Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)
TI - PROTEINS POCKETS ANALYSIS AND DESCRIPTION
SN - 978-989-674-019-1
AU - Cantoni V.
AU - Gatti R.
AU - Lombardi L.
PY - 2010
SP - 211
EP - 216
DO - 10.5220/0002725302110216