A novel graphical representation of proteins and its application

Physica A: Statistical Mechanics and its Applications

Volumn 391, Issue 1-2, 2012, Pages 93-99

  He, Ping An ^a   Wei, Jinzhou ^a   Yao, Yuhua ^a   Tie, Zhixin ^a  

^a ZHEJIANG SCI TECH UNIVERSITY   (China)

Author keywords

Correlation and significance analysis; Graphical representation; Numerical characterization; Protein; Similarity

Indexed keywords

PHYSICOCHEMICAL PROPERTIES; PROTEINS;

3D GRAPHICAL REPRESENTATION; COMPARISON RESULT; GRAPHICAL REPRESENTATIONS; ITS APPLICATIONS; NUMERICAL CHARACTERIZATION; PROTEIN SEQUENCES; SIGNIFICANCE ANALYSIS; SIMILARITY;

GRAPHIC METHODS;

EID: 80054015097     PISSN: 03784371     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.physa.2011.08.015     Document Type: Article

References (39)

1. S. Vinga, and J. Almeida Alignment-free sequence comparisona review Bioinformatics 19 2003 513 523
2. A. Nandy, M. Harle, and S.C. Basak Mathematical descriptors of DNA sequences: development and applications ARKIVOC 9 2006 211 238 (Pubitemid 44527394)
3. B. Liao, W. Zhu, J.W. Luo, and R.F. Li RNA secondary structure mathematical representation without degeneracy MATCH 57 2007 687 695
4. B. Liao, C. Zeng, F.Q. Li, and Y. Tang Analysis of similarity/ dissimilarity of DNA sequences based on dual nucleotides MATCH 59 2008 647 652
5. B. Liao, W.Y. Chen, X.M. Sun, and W. Zhu A binary coding method of RNA secondary structure and its application J. Comput. Chem. 30 2009 2205 2212
6. F.Q. Li, G.H. Huang, B. Liao, and Z.B. Liu HL curve: a novel 2-D graphical representation of protein sequences MATCH 61 2009 519 532
7. Z.B. Liu, B. Liao, and W. Zhu A new method to analyze the similarity based on dual nucleotides of the DNA sequence MATCH 61 2009 541 552
8. M. Randic, J. Zupan, and M. Novic On 3-D graphical representation of proteomics maps and their numerical characterization J. Chem. Inf. Comput. Sci. 41 2001 1339 1344
9. M. Randic, M. Novic, and M. Vracko Novel characterization of proteomics maps by sequential neighborhoods of protein spots J. Chem. Inf. Model. 45 2005 1205 1213 (Pubitemid 41476004)
10. M. Randic, F.A. Witzmann, V. Kodali, and S.C. Basak On the dependence of a characterization of proteomics maps on the number of protein spots considered J. Chem. Inf. Model. 46 2006 116 122 (Pubitemid 43282106)
11. H. González-Díaz, L.G. Pérez-Montoto, A. Duardo-Sanchez, E. Paniagua, S. Vázquez-Prieto, R. Vilas, M.A. Dea-Ayuela, F. Bolas-Fernández, C.R. Munteanu, J. Dorado, J. Costas, and F.M. Ubeira Generalized lattice graphs for 2D-visualization of biological information J. Theoret. Biol. 261 2009 136 147
12. R. Concu, M.A. Dea-Ayuela, L.G. Pérez-Montoto, F. Bolas-Fernández, F.J. Prado-Prado, G. Podda, E. Uriarte, F.M. Ubeira, and H. González-Díaz Prediction of enzyme classes from 3D structure: a general model and examples of experimentaltheoretic scoring of peptide mass fingerprints of Leishmania proteins J. Proteome Res. 8 2009 4372 4382
13. H.J. Jeffrey Chaos game representation of gene structure Nucleic Acids Res. 18 1990 2163 2170
14. M. Randic, J. Zupan, A.T. Balaban, D. Vikic-Topic, and D. Plavic Graphical representation of proteins Chem. Rev. 111 2011 790 862
15. M. Randic 2-D graphical representation of proteins based on virtual genetic code SAR QSAR Environ. Res. 15 2004 147 157 (Pubitemid 38641775)
16. M. Randic, J. Zupan, and A.T. Balaban Unique graphical representation of protein sequences based on nucleotide triplet codons Chem. Phys. Lett. 397 2004 247 252
17. M. Randic, D. Butina, and J. Zupan Novel 2-D graphical representation of proteins Chem. Phys. Lett. 419 2006 528 532 (Pubitemid 43220524)
18. B. Liao, B.Y. Liao, X.M. Sun, and Q.G. Zeng A novel method for similarity analysis and protein sub-cellular localization prediction Bioinformatics 26 2010 2678 2683
19. M. Randic 2-D graphical representation of proteins based on physico-chemical properties of amino acids Chem. Phys. Lett. 440 2007 291 295 (Pubitemid 46770670)
20. Y.H. Yao, Q. Dai, C. Li, P.A. He, X.Y. Nan, and Y.Z. Zhang Analysis of similarity/dissimilarity of protein sequences Protein 73 2008 864 871
21. J. Feng, and T.M. Wang Characterization of protein primary sequences based on partial ordering J. Theoret. Biol. 254 2008 752 755
22. S.S.T. Yau, C.L. Yu, and R. He A protein map and its application DNA Cell Biol. 27 2008 241 250 (Pubitemid 351655088)
23. J. Wen, and Y.Y. Zhang A 2D graphical representation of protein sequence and its numerical characterization Chem. Phys. Lett. 476 2009 281 286
24. M.I.A. el Maaty, M.M. Abo-Elkhier, and M.A. Abd Elwahaab 3D graphical representation of protein sequences and their statistical characterization Physica A 389 2010 4668 4676
25. P.A. He, X.F. Li, J.L. Yang, and J. Wang A novel descriptor for protein similarity analysis MATCH 65 2011 445 458
26. F.L. Bai, and T.M. Wang On graphical and numerical representation of protein sequences J. Biomol. Struct. Dyn. 23 2006 537 545
27. C. Li, X.Q. Yu, L. Yang, X.Q. Zheng, and Z.F. Wang 3-D maps and coupling numbers for protein sequences Physica A 388 2009 1967 1972
28. M. Randic, M. Vracko, M. Novic, and D. Plavic Spectral representation of reduced protein models SAR QSAR Environ. Res. 20 2009 415 427
29. Y.H. Yao, Q. Dai, L. Li, X.Y. Nan, P.A. He, and Y.Z. Zhang Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation J. Comput. Chem. 31 2010 1045 1052
30. M. Randic, K. Mehulic, D. Vukicevic, T. Pisanski, D. Vikic-Topic, and D. Plavic Graphical representation of proteins as four-color maps and their numerical characterization J. Mol. Graphics Modell. 27 2009 637 641
31. B. Liao, Y.S. Liu, R.F. Li, and W. Zhu Coronavirus phylogeny based on triplets of nucleic acids bases Chem. Phys. Lett. 421 2006 313 318
32. L. Zhang, B. Liao, D.C. Li, and W. Zhu A novel representation for apoptosis protein subcellular localization prediction using support vector machine J. Theoret. Biol. 259 2009 361 365
33. L. Xi, B. Liao, Q.G. Zeng, and J.W. Luo Protein functional class prediction using global encoding of amino acid sequence J. Theoret. Biol. 261 2009 290 293
34. Z.C. Wu, X. Xiao, and K.C. Chou 2D-MH: a web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids J. Theoret. Biol. 267 2010 29 34
35. M. Randic, A.T. Balaban, M. Novic, A. Zaloznik, and T. Pisanski A novel graphical representation of proteins Period. Biol. 107 2005 403 414 (Pubitemid 43067232)
36. M. Randic, J. Zupan, and D. Vikic-Topic On representation of proteins by star-like graphs J. Mol. Graphics Modell. 26 2007 290 305 (Pubitemid 46977263)
37. P.A. He A new graphical representation of similarity/dissimilarity studies of protein sequences SAR QSAR Environ. Res. 21 2010 571 580
38. P.A. He, Y.P. Zhang, Y.H. Yao, Y.F. Tang, and X.Y. Nan The graphical representation of protein sequences based on the physicochemical properties and its applications J. Comput. Chem. 31 2010 2136 2142
39. C.Z. Guo, and M.Q. Sun ClustalWA software for multiple sequence alignment of protein and nucleic acid sequence Biotechnol. Lett. 11 2000 146 149