CFP last date
20 May 2024
Call for Paper
June Edition
IJCA solicits high quality original research papers for the upcoming June edition of the journal. The last date of research paper submission is 20 May 2024

Submit your paper
Know more
The week's pick
Responsive image
Enhancing Privacy Preservation: Multi-Attribute Protection with P-Sensitive K-Anonymity

Twinkle Patel Kiran Amin
Random Articles
Reseach Article

Protein Data Representation: A Survey

by Ahmed S. Fadel, Mohamed Belal, Mostafa-sami M. Mostafa
journal cover thumbnail

International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 56 - Number 11
Year of Publication: 2012
Authors: Ahmed S. Fadel, Mohamed Belal, Mostafa-sami M. Mostafa
10.5120/8936-3075

Ahmed S. Fadel, Mohamed Belal, Mostafa-sami M. Mostafa . Protein Data Representation: A Survey. International Journal of Computer Applications. 56, 11 ( October 2012), 22-27. DOI=10.5120/8936-3075

@article{ 10.5120/8936-3075,
author = { Ahmed S. Fadel, Mohamed Belal, Mostafa-sami M. Mostafa },
title = { Protein Data Representation: A Survey },
journal = { International Journal of Computer Applications },
issue_date = { October 2012 },
volume = { 56 },
number = { 11 },
month = { October },
year = { 2012 },
issn = { 0975-8887 },
pages = { 22-27 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume56/number11/8936-3075/ },
doi = { 10.5120/8936-3075 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T20:58:34.957851+05:30
%A Ahmed S. Fadel
%A Mohamed Belal
%A Mostafa-sami M. Mostafa
%T Protein Data Representation: A Survey
%J International Journal of Computer Applications
%@ 0975-8887
%V 56
%N 11
%P 22-27
%D 2012
%I Foundation of Computer Science (FCS), NY, USA
Abstract

One of the critical issues in bioinformatics is the data structure used for representing the protein data; this representation is a base for the operations applied such as sequence alignment, structure alignment and motif finding. In this paper, a survey of different representations and well-known data structures used for protein data is presented from a computer science perspective. This work presents a survey and summarizes the efforts done for protein data representation and approximation. Hence, it could be a basic reference for research that is aiming to develop applications in the field of bioinformatics.

References
  1. V Sheth, "Visualization of protein 3D structures in reduced representation with simultaneous display of intra and inter-molecular interactions," phdthesis 2009.
  2. Fabian Schwarzer and Itay Lotan, "Approximation of Protein Structure for Fast Similarity measures," in Proceedings of the seventh annual international conference on Research in computational molecular biology RECOMB '03, 2003.
  3. M. Peto, T. Z. Sen, R. L. Jernigan, and A. Kloczkowski, "Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices," The Journal of chemical physics, vol. 127, p. 044101, 2007.
  4. K. Marsolo and S. Parthasarathy, "On the use of structure and sequence-based features for protein classification and retrieval," Knowledge and Information Systems, vol. 14, no. 1, pp. 59-80, 2008.
  5. Hayashi, Sushmita Mitra, and Yoichi, "Bioinformatics With Soft Computing," IEEE TRANSACTIONS ON SYSTEMS, MAN, AND CYBERNETICS, vol. 36, no. 5, 2006.
  6. M S Abual-Rub and R Abdullah, "A Survey of Protein Fold Recognition Algorithms," Journal of Computer Science, vol. 4, pp. 768--776, 2008.
  7. A Via, F Ferre, B Brannetti, and M Helmer-Citterich*, "Protein surface similarities: a survey of methods to describe and compare protein surfaces," Cellular and Molecular Life Sciences, vol. 57, pp. 1970--1977, 2000.
  8. C Notredame, "Recent progress in multiple sequence alignment: a survey," Pharmacogenomics, vol. 3, pp. 131--144, 2002.
  9. Z Xing, J Pei, and E Keogh, "A brief survey on sequence classification," ACM SIGKDD Explorations Newsletter, vol. 12, pp. 40--48, 2010.
  10. Z Xiu-fen, P Zi-shu, K Li-shan, and Z Chu-yu, "The evolutionary computation techniques for protein structure prediction: A survey," Wuhan University Journal of Natural Sciences, vol. 8, pp. 297--302, 2003.
  11. CA Floudas, HK Fung, SR McAllister, M Monnigmann, and R Rajgaria, "Advances in protein structure prediction and de novo protein design: A review," Chemical Engineering Science, vol. 61, pp. 966--988, 2006.
  12. G Pandey, V Kumar, and M Steinbach, "Computational approaches for protein function prediction: A survey," techreport 2006.
  13. CA Floudas, "Computational methods in protein structure prediction," Biotechnology and bioengineering, vol. 97, pp. 207--213, 2007.
  14. V Arjunan, S Nanda, S Deris, and M Illias, "Literature survey of protein secondary structure prediction," Jurnal Teknologi C, pp. 63--72, 2001.
  15. J Yu and F Fotouhi, "Computational approaches for predicting protein--protein interactions: a survey," Journal of Medical Systems, vol. 30, pp. 39--44, 2006.
  16. J Liang, "Computation of protein geometry and its applications: Packing and function prediction," Computational Methods for Protein Structure Prediction and Modeling, pp. 181--206, 2007.
  17. Jean-Michel Claverie and Cedric Notredame, Bioinformatics for Dummies, 2nd edition. : wiley publishing, 2007.
  18. Regina Bailey. (2011) Protein Function. [Online]. http://biology. about. com/od/molecularbiology/a/aa101904a. htm
  19. Wolfgang Kabsch and Christian Sander, "Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features," Biopolymers, vol. 22, pp. 2577--2637, 1983.
  20. (2012) RCSB PDB. [Online]. http://www. rcsb. org/pdb/home/home. do
  21. Dong Xu, Hua Li, and Tongjun Gu, "Shape Representation and Invariant Description of Protein Tertiary Structure," Advances in Geometric Modeling and Processing, vol. 2, no. 5, pp. 556-562, 2008.
  22. Dong Xu, and Jie Liang Ying Xu, "Computational methods for protein structure prediction," Biotechnology and bioengineering, vol. 97, pp. 207-213, 2007.
  23. Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen, "Automatic Classification of Protein Structures Based on Convex Hull Representation," in Theory and Applications of Models of Computation. Berlin : Springer, 2006, pp. 505-514.
  24. Saul B Needleman and Christian D Wunsch, "A general method applicable to the search for similarities in the amino acid sequence of two proteins," Journal of Molecular Biology, vol. 48, pp. 443 - 453, 1970.
  25. TF Smith and MS Waterman, "Identification of common molecular subsequences," Journal of Molecular Biology, vol. 147, pp. 195 - 197, 1981.
  26. J Razmara, S Deris, and S Parvizpour, "TS-AMIR: A Topology String Alignment Method for Intensive Rapid Protein Structure Comparison," Algorithms for Molecular Biology, vol. 7, p. 4, 2012.
  27. Feng Gao and Mohammed J. Zaki, "PSIST:A scalable approach to indexing protein structures using suffix trees," Journal of Parallel and Distributed Computing, vol. 68, pp. 54--63, 2008.
  28. T Shibuya, "Geometric suffix tree: Indexing protein 3-D structures," Journal of the ACM (JACM), vol. 57, p. 15, 2010.
  29. A. Ma'ayan, "Network integration and graph analysis in mammalian molecular systems biology," Systems Biology, IET, vol. 2, pp. 206-221, 2008.
  30. Phung, Do Phuc, and Nguyen Thi Kim, "Visualization of the Similar Protein Structures Using SOM Neural Network and Graph Spectra," Intelligent Information and Database Systems, pp. 258-267, 2010.
  31. Hyunjung Shin, Koji Tsuda, and Bernhard Scholkopf, "Protein functional class prediction with a combined graph," Expert Systems with Applications, vol. 36, pp. 3284--3292, 2009.
  32. S. S. Abeysinghe, T. Ju, W. Chiu, and M. Baker, "Shape modeling and matching in identifying protein structure from low-resolution images," Proceedings of the 2007 ACM symposium on Solid and physical modeling, pp. 223--232, 2007.
  33. M. Vassura, L. Margara, P. Fariselli, and R. Casadio, "A graph theoretic approach to protein structure selection," in Applications of Fuzzy Sets Theory. Berlin / Heidelberg: Springer, 2007, pp. 497-504.
  34. V. Tsatsaias, P. Daras, and M. G. Strintzis, "3D protein classification using topological, geometrical and biological information," in IEEE International Conference on Image Processing, 2007.
  35. D. M. Strickland, E. Barnes, and J. S. Sokol, "Optimal Protein Structure Alignment Using Maximum Cliques," Operations research, vol. 53, pp. 389-402, 2005.
  36. William Taylor and Andras Aszodi, Protein geomtry,classification,topology and symmetry. : Institute of physics publishing, 2005.
  37. P. H. and Scott, G. and Shyu, C. R. Chi, "A fast protein structure retrieval system using image-based distance matrices and multidimensional index," in Fourth IEEE Symposium on Bioinformatics and Bioengineering, 2004. BIBE 2004. Proceedings. , vol. 15, 2005, pp. 522-529.
  38. A. Sacan, I. H. Toroslu, and H. Ferhatosmanoglu, "Distance-based Indexing of Residue Contacts for Protein Structure Retrieval and Alignment," in 8th IEEE International Conference on BioInformatics and BioEngineering, 2008, pp. 1-7.
  39. J Vesterstrøm and W R Taylor, "Flexible secondary structure based protein structure comparison applied to the detection of circular permutation," Journal of Computational Biology, vol. 13, pp. 43--63, 2006.
Index Terms

Computer Science
Information Sciences

Keywords

Protein representation Protein structure Data structure Data reduction Protein structure approximation

Powered by PhDFocusTM