SEGMENTATION OF SES FOR PROTEIN STRUCTURE ANALYSIS

Virginio Cantoni, Riccardo Gatti, Luca Lombardi

2010

Abstract

The morphological complementarities of molecular surfaces provides insights for the identification and evaluation of binding sites. A quantitative characterization of these sites is an initial step towards protein based drug design. The final goal of the activity here presented is to provide a method that allows the identification of sites of possible protein-protein and protein-ligand interaction on the basis of the geometrical and topological structure of protein surfaces. The goal is to discover complementary regions (that is with concave and convex segments that match each others) among different molecules. In particular, we are considering the first step of this process: the segmentation of the protein surface in protuberances and cavities through an approach based on an analysis of the molecule Convex Hull and on the Distance Transform.

References

  1. Akutsu T, 1996. Protein structure alignment using dynamic programming and iterative improvement. In IEICE Trans. Inf. and Syst., Vol. E'-D, pp. 1-8.
  2. Barber CB, Dobkin DP, and Huhdanpaa H, 1996. The Quickhull Algorithm for Convex Hull. In ACM Transactions on Mathematical Software, Vol. 22, N. 4, pp. 469-483.
  3. Bock ME, Garutti C, Guerra C, 2007. Spin image profile: a geometric descriptor for identifying and matching protein cavities. In Proc. of CSB, San Diego.
  4. Bock ME, Garutti C, Guerra, C, 2008. Cavity detection and matching for binding site recognition. In Theoretical Computer Science, doi:10.1016/j.tcs.2008.08.018.
  5. Borgefors G and Sanniti di Baja G, 1996. Analyzing Nonconvex 2D and 3D Patterns. In Computer Vision and image Understanding, vol. 63, N. 1, pp. 145-157.
  6. Brady GP, Stouten PFW, 2000. Fast prediction and visualization of protein binding pockets with PASS. In J Comput-Aided Mol Des, 14, pp. 383-401.
  7. Cantoni V, Gatti R, and Lombardi L, 2009. Towards Protein Interaction Analysis through Surface Labeling. ICIAP 2009, in press.
  8. Coleman RG, Sharp KA, 2006. Travel Depth, a New Shape Descriptor for Macromolecules: Application to Ligand Binding. In J. Mol. Biol., Vol. 362, pp. 441- 458. 1MK5 1A0Q 1ATJ PDBbind, 29 di pg 451, 1H2R
  9. Edelsbrunner H, Liang J and Woodward C, 1998. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. In protein Science 7, pp. 1884-1897.
  10. Frome A, Huber D, Kolluri R, Baulow T and Malik J, 2004. Recognizing Objects in Range Data Using Regional Point Descriptors. In Computer Vision - ECCV, pp. 224-237.
  11. Giard J, Rondao Alface Patrice, Macq B, 2008. Fast and accurate travel depth estimation for protein active site prediction. In SPIE Electronic Imaging 2008, San Jose, California USA, San Jose CĂ©lifornia, USA, 6812, pp. 0Q-10Q.
  12. Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA and Thornton JM, 2006. A Method for Localizing Ligand Binding Pockets in Protein Structures. In PROTEINS: Structure, Function, and Bioinformatics, 62, pp. 479- 488.
  13. Meier R, Ackermann F, Hermann G, Posch S, and Sagerer G, 1995. Segmentation of molecular surfaces based on their convex hull. In Proceedings IEEE International Conference on Image Processing, pp. 552-554. 2utg
  14. Shulman-Peleg A, Nussinov R and Wolfson H, 2004. Recognition of Functional Sites in Protein Structures. In J. Mol. Biol., 339, pp. 607-633.
  15. Xie L and Bourne PE, 2007. A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites. In BMC Bioinformatics, 8 (Suppl 4):S9.
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Paper Citation


in Harvard Style

Cantoni V., Gatti R. and Lombardi L. (2010). SEGMENTATION OF SES FOR PROTEIN STRUCTURE ANALYSIS . In Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010) ISBN 978-989-674-019-1, pages 83-89. DOI: 10.5220/0002590900830089


in Bibtex Style

@conference{bioinformatics10,
author={Virginio Cantoni and Riccardo Gatti and Luca Lombardi},
title={SEGMENTATION OF SES FOR PROTEIN STRUCTURE ANALYSIS},
booktitle={Proceedings of the First International Conference on Bioinformatics - Volume 1: BIOINFORMATICS, (BIOSTEC 2010)},
year={2010},
pages={83-89},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002590900830089},
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 - SEGMENTATION OF SES FOR PROTEIN STRUCTURE ANALYSIS
SN - 978-989-674-019-1
AU - Cantoni V.
AU - Gatti R.
AU - Lombardi L.
PY - 2010
SP - 83
EP - 89
DO - 10.5220/0002590900830089