On graphical representation of trans-membrane proteins

SAR and QSAR in Environmental Research

Volumn 23, Issue 3-4, 2012, Pages 327-343

  Randic M ^a   Novic M ^a   Choudhury, A Roy ^a   Plavsic D ^b  

^a NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^b RUDER BO KOVI INSTITUTE   (Croatia)

Author keywords

amino acid adjacency matrix; protein maps; trans membrane proteins

Indexed keywords

AMINO ACIDS; BIOLOGICAL MEMBRANES; GRAPH THEORY; GRAPHIC METHODS;

ADJACENCY MATRIX; AMINO ACID ADJACENCY MATRIX; AMINO-ACIDS; GRAPHICAL REPRESENTATIONS; MATRIX; MATRIX ELEMENTS; NOVEL PROTEINS; PRIMARY STRUCTURES; PROTEIN MAP; TRANS-MEMBRANE PROTEINS;

PROTEINS;

EID: 84860270264     PISSN: 1062936X     EISSN: 1029046X     Source Type: Journal    
DOI: 10.1080/1062936X.2012.658083     Document Type: Article

References (60)

1. Hamori, E and Ruskin, J. 1983. H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences. J. Biol. Chem., 258: 1318-1327.
2. Hamori, E. 1989. Graphical representation of long DNA sequences by methods of H curves, current results and future aspects. BioTechniques., 7: 710-720.
3. Hamori, E. 1994. Visualization of biological information encoded in DNA, in Frontiers of Scientific Visualization, Vol. 3, 91-121. New York: J. Wiley and Sons.
4. Jeffrey, HJ. 1990. Chaos game representation of gene structure. Nucleic Acid Res., 18: 2163-2170.
5. Barnsley, M. 1988. Fractals Everywhere, Boston, MA: Academic Press.
6. Nandy, A. 1994. A new graphical representation and analysis of DNA sequence structure: I. Methodology and application to globin genes. Current Sci., 66: 309-313.
7. Nandy, A. 1996. Graphical analysis of DNA sequence structure: III. Indications of evolutionary distinctions and characteristics of introns and exons. Current Sci., 70: 661-668.
8. Nandy, A. 1996. Two-dimensional graphical representation of DNA sequences and intron-exon discrimination in intron-rich sequences. Comput. Appl. Biosci., 12: 55-62.
9. Roy, A, Raychaudhary, C and Nandy, A. 1998. Novel techniques of graphical representation and analysis of DNA-A review. J. Biosci., 23: 55-71.
10. Leong, PM and Morgenthaler, S. 1995. Random walk and gap plots of DNA sequences. Comput. Appl. Biosci., 12: 503-511.
11. Randić, M. 2000. Condensed representation of DNA primary sequences. J. Chem. Inf. Comput. Sci., 40: 50-56.
12. Randić, M. 2000. On characterization of DNA primary sequences by condensed matrix. Chem. Phys. Lett., 317: 29-34.
13. Randić, M and Vračko, M. 2000. On the similarity of DNA primary sequences. J. Chem. Inf. Comput. Sci., 40: 599-606.
14. Randić, M, Guo, X and Basak, SC. 2001. Characterization of DNA based on occurrence of triplets of nucleic bases. J. Chem. Inf. Comput. Sci., 41: 619-626.
15. Jayalakshmi, R, Natarajan, R and Vivekanandan, M. 2011. Extension of molecular similarity analysis approach to classification of DNA sequences using DNA descriptors. SAR QSAR Environ. Res., 22: 21-34.
16. Randić, M and Zupan, J. 2004. Highly compact 2-D graphical representation of DNA sequences. SAR QSAR Environ. Res., 15: 191-205.
17. Randić, M, Vračko, M, Zupan, J and Novič, M. 2003. Compact 2-D graphical representation of DNA. Chem. Phys. Lett., 373: 558-562.
18. Randić, M. 2001. On graphical representation of proteomics and their numerical characterization. J. Chem. Inf. Comput. Sci., 41: 1330-1338.
19. Randić, M, Zupan, J and Novič, M. 2001. On 3-D graphical representation of proteomics maps. J. Chem. Inf. Comput. Sci., 41: 1339-1334.
20. Randić, M, Witzmann, F, Vračko, M and Basak, SC. 2001. On characterization of proteomics maps and chemically induced changes in proteome using matrix invariants: Application to peroxisome proliferators. Med. Chem. Rev., 10: 456-479.
21. Randić, M. 2002. A graph theoretical characterization of proteomics maps. Int. J. Quantum Chem., 90: 848-858.
22. Randić, M, Novič, M and Vračko, M. 2002. On characterization of dose variations of 2-D proteomics maps by matrix invariants. J. Proteome Res., 1: 217-226.
23. Randić, M. 2003. Quantitative characterization of proteomics maps by matrix invariants, in Handbook of Proteomics Methods, Totowa, NJ: Humana Press Inc.
24. Randić, M, Lerš, N, Plavšić, D and Basak, SC. 2004. On invariants of a 2-D proteome map derived from neighborhood graphs. J. Proteome Res., 3: 778-785.
25. Randić, M and Basak, SC. 2004. On similarity of proteome maps. Med. Chem. Res., 13: 800-811.
26. Randić, M, Zupan, J, Novič, M, Gute, BD and Basak, SC. 2004. Novel matrix invariants for characterization of changes of proteomics maps. SAR QSAR Environ. Res., 15: 147-157.
27. Randić, M. 2006. Quantitative characterization of proteome: Dependence on the number of proteins considered. J. Proteome Res., 5: 1575-1579.
28. Randić, M and Estrada, E. 2005. Order from chaos: Observing hormesis at the proteome level. J. Proteome Res., 4: 2133-2136.
29. Randić, M, Novič, M and Vračko, M. 2005. Novel characterization of proteomics maps by sequential neighborhood of protein spots. J. Chem. Inf. Model., 45: 1205-1213.
30. Randić, M, Lerš, N, Vukučević, D, Plavšić, D, Gute, BD and Basak, SC. 2005. Canonical labeling of proteome maps. J. Proteome Res., 4: 1347-1352.
31. Randić, M, Novič, M, Vračko, M and Plavšić, D. 2010. Study of proteome maps using partial ordering. J. Theor. Biol., 266: 21-28.
32. Randić, M, Witzmann, FA, Kodali, V and Basak, SC. 2006. Dependence of a characterization of proteomics maps on the number of protein spots considered. J. Chem. Inf. Model., 46: 116-122.
33. Randić, M and Orel, R. 2011. On numerical characterization of proteomics maps based on partitioning of 2-D maps into Voronoi regions. J. Math. Chem., 49: 1759-1768.
34. Randić, M. 2004. 2-D graphical representation of proteins based on virtual genetic code. SAR QSAR Environ. Res., 15: 147-157.
35. Randić, M, Vračko, M, Lerš, N and Plavšić, D. 2003. Novel 2-D graphical representation of DNA sequences and their numerical characterization. Chem. Phys. Lett., 368: 1-6.
36. Randić, M, Vračko, M, Lerš, N and Plavšić, D. 2003. Analysis of similarity/dissimilarity of DNA based on novel 2-D graphical representation. Chem. Phys. Lett., 371: 202-207.
37. Randić, M, Vračko, M, Novič, M and Plavšić, D. 2009. Spectral representation of reduced protein models. SAR QSAR Environ. Res., 20: 415-427.
38. Zupan, J and Randić, M. 2005. Algorithm for coding DNA sequences into "Spectrum-like" and "Zigzag" representations. J. Chem. Inf. Model., 45: 309-313.
39. Randić, M. 2004. Graphical representation of DNA as 2-D map. Chem. Phys. Lett., 386: 468-471.
40. He, P. 2010. A new graphical representation of similarity/dissimilarity studies of protein sequences. SAR QSAR Environ. Res., 21: 571-580.
41. Randić, M, Lerš, N, Plavšić, D, Basak, SC and Balaban, AT. 2005. Four-color map representation of DNA or RNA sequences and their numerical characterization. Chem. Phys. Lett., 407: 205-208.
42. Randić, M, Mehulić, K, Vukičević, D, Pisanski, T, Vikić-Topić, D and Plavšić, D. 2009. Graphical representation of proteins as four-color maps and their numerical characterization. J. Mol. Graph. Model., 27: 637-641.
43. Randić, M, Zupan, J, Balaban, AT, Vikić-Topić, D and Plavšić, D. 2011. Graphical representation of proteins. Chem. Rev., 111: 790-862.
44. Randić, M. 2008. On a geometry-based approach to protein sequence alignment. J. Math. Chem., 43: 756-772.
45. Randić, M, Zupan, J and Vikić-Topić, D. 2007. Graphical representation of proteins by star-like graphs. J. Mol. Graphics Model., 26: 290-305.
46. Horvat, B, Pisanski, T and Randić, M. 2008. Terminal polynomials and star-like graphs. Commun. Math. Comput. Chem., 60: 493-512.
47. Randić, M, Zupan, J and Balaban, AT. 2004. Unique graphical representation of protein sequences based on nucleotide triplet codons. Chem. Phys. Lett., 397: 247-252.
48. Randić, M, Butina, D and Zupan, J. 2006. Novel 2-D graphical representation of proteins. Chem. Phys. Lett., 419: 528-532.
49. Randić, M, Lerš, N, Plavšić, D and Basak, SC. 2004. Characterization of 2-D proteome maps based on the nearest neighborhoods of spots. Croat. Chem. Acta., 77: 345-351.
50. Randić, M, Novič, M and Vračko, M. 2008. On novel representation of proteins based on amino acid adjacency matrix. SAR QSAR Environ. Res., 19: 339-349.
51. Nandy, A, Harle, M and Basak, SC. 2006. Mathematical descriptors of DNA sequences: Development and applications. Arkivoc., 9: 211-238.
52. Randić, M. 1975. Characterization of molecular branching. J, Am. Chem. Soc., 97: 6609-6615.
53. Kier, LB, Murray, WJ, Randić, M and Hall, LH. 1976. Molecular connectivity V: Connectivity series concept applied to density. J. Pharm. Sci., 65: 1226-1230.
54. Kier, LB and Hall, LH. 1976. Molecular Connectivity in Chemistry and Drug Research, New York: Academic Press.
55. Kier, LB and Hall, LH. 1986. Molecular Connectivity in Structure Activity Analysis, London: John Wiley.
56. Randić, M, Kleiner, AF and DeAlba, LM. 1994. Distance/distance matrices. J. Chem. Inf. Comput. Sci., 34: 277-286.
57. Zaretskii, K. 1965. Constructing a tree on the basis of a set of distances between the hanging vertices. Usp. Math. Nauk., 20: 90-92.
58. Read, RC. 1981. A survey of graph generation techniques. Lect. Notes Math., 884: 77-89.
59. Rouse Ball, WW. 1922. Mathematical Recreations and Essays, London: MacMillan and Co. Ltd.
60. Knop, JV, Müller, WR, Szymanski, K and Trinajstić, N. Computer Generation of Certain Classes of Molecules, SKTH/Kemija u Industriji, Zagreb, Croatia, 1985