Abstract
Study of the morphology of proteins, and their 3D structure, supports investigations of their functions and represents an initial step towards protein-based drug design. The goal of this paper is to define techniques, based on the geometrical and topological structure of protein surfaces, for the detection and analysis of sites of potential protein-protein and protein-ligand interactions. Two protein representation modalities based on the Concavity Tree (CT) and the Enriched Complex Extended Gaussian Image (EC-EGI) are considered. In particular, the concavity tree, in which the interface is usually extended and roughly planar, is considered to be better suited to protein-protein interaction studies. Instead, the EGI is more suited to protein-ligand interactions, in which the small ligand molecule usually has to fit into the protein cavity. In fact, the histogram of the orientations is better suited to representing a mainly convex object and its dual matching region (the cavity). Both these data structures are open, and can be easily integrated with biochemical features.
Similar content being viewed by others
References
A. Shulman-Peleg, S. Mintz, R. Nussinov, H.J. Wolfson, Protein-protein interfaces: Recognition of similar spatial and chemical organizations in Algorithms in Bioinformatics, edited by I. Jonassen, J. Kim, Lecture Notes in Computer Science, Vol. 3240 (Springer Berlin Heidelberg, 2004) pp. 194–205.
C. Garutti, C. Guerra, M.E. Bock, Effective labeling of molecular surface points for cavity detection and location of putative binding sites (World Scientific, 2007) chapt. 28, pp. 263–274.
A. Frome, D. Huber, R. Kolluri, T. Bulow, J. Malik, Recognizing objects in range data using regional point descriptors, in Proceedings of the European Conference on Computer Vision (ECCV) (2004) pp. 224–237.
F. Glaser, R. Morris, R. Najmanovich, R. Laskowski, J. Thornton, Proteins 62, 479 (2006).
S.R. Sternberg, Language and architecture for parallel image processing, in Proceedings of the Conference on Pattern Recognition in Practice (Amsterdam, 1980).
S.R. Sternberg, Overview of image algebra and related issues (Academic Press, 1985) p. 35.
J. Serra, Image Analysis and Mathematical Morphology (Academic Press, 1982).
M.L. Connolly, Science 221, 709 (1983).
M.L. Connolly, J. Appl. Crystallogr. 16, 548 (1983).
M. Masuya, Shape Analysis of Protein Molecule and Ligand-Recepter Docking StudiesUsing Mathematical Morphology, PhD thesis, The University of Tokyo (1996).
K. Takeshi, Multi-scale pocket detection on protein surface using 3d image processing technique, Tech. rep., IPSJ SIG (2006).
H.-T. Chang, C.-H. Liu, T.-W. Pai, J. Mol. Recognit. 21, 431 (2008).
M. Prisant, Ray-representation formalism for geometric computations on protein solid models, in Applied Computational Geometry Towards Geometric Engineering, edited by M. Lin, D. Manocha, Lecture Notes in Computer Science, Vol. 1148 (Springer, Berlin Heidelberg, 1996) pp. 79–90.
R.G. Coleman, K.A. Sharp, J. Mol. Biol. 362, 441 (2006).
R.G. Coleman, K.A. Sharp, J. Chem. Inf. Model. 50, 589 (2010).
J. Sklansky, IEEE Trans. Comp. 21, 1355 (1972).
B. Batchelor, IEE J. Comput. Digit. Tech. 2, 157 (1979).
G. Borgefors, G.S. di Baja, Comput. Vis. Image Underst. 63, 145 (1996).
V. Cantoni, R. Gatti, L. Lombardi, Segmentation of ses for protein structure analysis, in Proceedings of the 1st International Conference on Bioinformatics (2010) pp. 83–89.
R. Laskowski, N. Luscombe, M. Swindells, J. Thornton, Protein Sci. 5, 2438 (1996).
J. Giard, P. Rondao Alface, B. Macq, Proc. SPIE681268120Q2008.
C. Arcelli, G.S. di Baja, Polygonal covering and concavity tree of binary digital pictures, in Proceedings of the international conference MECO78 (1978) pp. 292–297.
V. Cantoni, R. Gatti, L. Lombardi, Towards protein interaction analysis through surface labeling, in Proceedings of the 15th International Conference on image analysis and processing (2009) pp. 604–612.
F. Glaser, Y. Rosenberg, A. Kessel, T. Pupko, N. Bental, Proteins 58, 610 (2005).
B. Horn, Extended gaussian images, in Proceedings of the IEEE, Vol. 72 (1984) pp. 1671–1686.
S. Kang, K. Ikeuchi, IEEE Trans. Pattern Anal. Mach. Intell. 15, 707 (1993).
H. Matsuo, A. Iwata, 3-D object recognition using MEGI model from range data, in Proceedings of the 12th IAPR International Conference on Pattern Recognition, Vol. 1 (IEEE, 1994) p. 843.
D. Wang, J. Zhang, H.-S. Wong, Y. Li, 3d model retrieval based on multi-shell extended gaussian image, in Advances in Visual Information Systems, edited by G. Qiu, C. Leung, X. Xue, R. Laurini, Lecture Notes in Computer Science, Vol. 4781 (Springer, Berlin Heidelberg, 2007) pp. 426–437.
J. Zhang, D. Wang, H.S. Wong, 3d model representation using adaptive volumetric extended gaussian image, in Proceedings of the 6th ACM International Conference on Image and Video Retrieval (New York, NY, USA, 2007) pp. 480–485.
Z. Hu, R. Chung, K. Fung, Machine Vision Appl. 21, 177 (2010).
S.B. Kang, K. Ikeuchi, Determining 3-d object pose using the complex extended Gaussian image, in Proceedings of the 1991 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR ’91) (1991) pp. 580–585.
J. Zhang, H.-S. Wong, Z. Yu, 3d model metrieval based on volumetric extended gaussian image and hierarchical self organizing map, in Proceedings of the 14th Annual ACM International Conference on Multimedia (New York, NY, USA, 2006) pp. 121–124.
V. Cantoni, A. Gaggia, R. Gatti, L. Lombardi, Geometrical constraints for ligand positioning, in Proceedings of the 2nd International Conference on Bioinformatics (SciTePress, 2011).
Author information
Authors and Affiliations
Corresponding author
Additional information
Contribution to the Focus Point on “Pattern Recognition Tools for Proteomics” edited by V. Cantoni.
Rights and permissions
About this article
Cite this article
Cantoni, V., Gaggia, A., Gatti, R. et al. Structural representation of data structures. Eur. Phys. J. Plus 129, 133 (2014). https://doi.org/10.1140/epjp/i2014-14133-0
Received:
Accepted:
Published:
DOI: https://doi.org/10.1140/epjp/i2014-14133-0