Mathematical biodescriptors of proteomics maps: Background and applications

Current Opinion in Drug Discovery and Development

Volumn 11, Issue 3, 2008, Pages 320-326

  Basak, S C ^a   Gute, B D ^a  

^a Natural Resources Research Institute   (United States)

Author keywords

Biodescriptor; Biomarker; Biosignature; D D matrix; Embedded graph; Graph invariant; Leading eigenvalue; Map information content; Map similarity; Proteomics map; Zigzag graph

Indexed keywords

CLOFIBRATE; PERFLUORODECANOIC ACID; PERFLUOROOCTANOIC ACID; PHTHALIC ACID BIS(2 ETHYLHEXYL) ESTER;

DNA SEQUENCE; INFORMATION SCIENCE; MATHEMATICS; NONHUMAN; PROTEOMICS; REVIEW; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ANIMALS; BIOLOGICAL MARKERS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DRUG DESIGN; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; HYDROCARBONS; INFORMATION THEORY; KERATINOCYTES; PROTEINS; PROTEOMICS; TECHNOLOGY, PHARMACEUTICAL;

EID: 42449153333     PISSN: 13676733     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (37)

1. Randić M, Vracko M, Nandy A, Basak SC: On 3D graphical representation of DNA primary sequences and their numerical characterization. J Chem Inf Comput Sci (2000) 40(5):1235-1244. •• The first report on the formulation of mathematical invariants of DNA sequences.
2. Nandy A, Basak SC: A simple numerical descriptor for quantifying effect of toxic substances on DNA sequences. J Chem Inf Comput Sci (2000) 40(4):915-919.
3. Randić M, Basak SC: Characterization of DNA primary sequences based on the average distance between bases. J Chem Inf Comput Sci (2001) 41(3):561-568.
4. Guo X, Randić M, Basak SC: A novel 2D graphical representation of DNA sequences of low degeneracy. Chem Phys Lett (2001) 350(1):106-112.
5. Randić M, Guo X, Basak SC: On the characterization of DNA primary sequences by triplet of nucleic acid bases. J Chem Inf Comput Sci (2001) 41(3):619-626.
6. Nandy A, Nandy P, Basak SC: Quantitative descriptor for SNP related gene sequences. Internet Electron J Mol Des (2002) 1(7):367-373. •• Describes the use of graphical (plotting) methods in the characterization of the structure and function of gene sequences.
7. Gates MA: A simple way to look at DNA. J Theor Biol (1986) 119(3):319-328.
8. Jeffrey HJ: Chaos game representation of gene structure. J Nucleic Acids Res (1990) 18(8):2163-2170.
9. Nandy A: A new graphical representation and analysis of DNA sequence structure. I: Methodology and application to globin genes. Curr Sci (1994) 66(4):309-314.
10. Nandy A: Two-dimensional graphical representation of DNA sequences and intron-exon discrimination in intron-rich sequences. Comput Appl Biosci (1996) 12(1):55-62.
11. Nandy A, Harle M, Basak SC: Mathematical descriptors of DNA sequences: Development and application. ARKIVOC (2006) (ix):211-238. • Provides an exhaustive review of the published studies on DNA invariants that were stimulated by the publication of reference [1••].
12. Leong PM, Morgenthaler S: Random walk and gap plots of DNA sequences. Comput Appl Biosci (1995) 11(5):503-507.
13. Raychaudhury C, Nandy A: Indexing scheme and similarity measures for macromolecular sequences. J Chem Inf Comput Sci (1999) 39(2):243-247.
14. Randić M, Witzmann F, Vracko M, Basak SC: On characterization of proteomics maps and chemically induced changes in proteomes using matrix invariants: Application to peroxisome proliferators. Med Chem Res (2001) 10(7-8):456-479. •• The first publication on the formulation of graph-theoretic proteomics biodescriptors.
15. Bunge M: Method, Model and Matter. D Reidel Publishing Company, Dordrecht, Holland & Boston, MA, USA (1973).
16. Harary F: Graph Theory. Addison-Wesley, Reading, MA, USA (1969).
17. Harary F: Graph theory as applied mathematics. J Graph Theory (1986) 10(3):iii-iv.
18. Trinajstic N: Chemical Graph Theory, 2nd Edition. CRC Press, Boca Raton, FL, USA (1992).
19. Basak SC, Magnuson VR, Niemi GJ, Regal RR: Determining structural similarity of chemicals using graph-theoretic indices. Discrete Appl Math (1988) 19(1-3):17-44.
20. Randić M, Basak SC: A comparative study of proteomics maps using graph theoretical biodescriptors. J Chem Inf Comput Sci (2002) 42(5):983-992.
21. Randić M, Zupan J, Novic M, Gute BD, Basak SC: Novel matrix invariants for characterization of changes of proteomics maps. SAR QSAR Environ Res (2002) 13(7-8):689-703.
22. Bajzer Z, Randić M, Plavsić D, Basak SC: Novel map descriptors for characterization of toxic effects in proteomics maps. J Mol Graph Model (2003) 22(1):1-9.
23. Randić M, Lers N, Plavsić D, Basak SC: On invariants of a 2D proteome map derived from neighborhood graphs. J Proteome Res (2004) 3(4):778-785.
24. Balasubramanian K, Khokhani K, Basak SC: Complex graph matrix representations and characterizations of proteomic maps and chemically induced changes to proteomes. J Proteome Res (2006) 5(5):1133-1142.
25. Randić M, Novic M, Vracko M: On characterization of dose variations of 2D proteomics maps by matrix invariants. J Proteome Res (2002) 1(3):217-226.
26. Basak SC, Gute BD, Witzmann F: Information-theoretic biodescriptors for proteomics maps: Development and applications in predictive toxicology. WSEAS Trans Inf Sci Appl (2005) 2(7):996-1001. •• Describes the formulation of a new information-theoretic biodescriptor.
27. Basak SC, Gute BD, Geiss KT, Witzmann FA: Information-theoretic biodescriptors for proteomics maps: Application to rodent hepatotoxicity. In: Computation in Modern Science and Engineering, Proceedings of the International Conference on Computational Methods in Science and Engineering (ICCMSE) 2007. Simos TE, Maroulis G (Eds), American Institute of Physics, Melville, NY, USA (2007):10-13.
28. Basak SC, Gute BD, Monteiro-Riviere NA, Witzmann FA: Characterization of toxicoproteomics maps for mixtures and individual toxicants using information-theoretic approach. In: Principles and Practice of Mixture Toxicity. Mumtaz MM (Ed), Wiley-VCH Verlag GmbH & Co KGaA, Weinheim, Germany (2008): in press. • Describes the use of information-theoretic biodescriptors in the characterization of the effects of complex mixtures, such as JP-8.
29. Shannon CE: A mathematical theory of communication. Bell Syst Tech J (1948) 27(7):379-423.
30. Basak SC: Information-theoretic indices of neighborhood complexity and their applications. In: Topological Indices and Related Descriptors in QSAR and QSPR. Devillers J, Balaban AT (Eds), Gordon and Breach Science Publishers, The Netherlands (1999):563-593.
31. Bonchev D, Randić M: Shannon's entropy of proteomic 2D-gel maps. Chem Phys Lett (2003) 372(3-4):548-552. •• Describes the formulation of a new information-theoretic biodescriptor.
32. Vracko M, Basak SC: Similarity study of proteomic maps. Chemometr Intell Lab Syst (2004) 70(1):33-38. •• Presents a novel method for measuring the similarity/dissimilarity of proteomics maps.
33. Vracko M, Basak SC, Geiss K, Witzmann F: Proteomics maps - Toxicity relationship of halocarbons studied with similarity index and genetic algorithm. J Chem Inf Model (2006) 46(1):130-136.
34. Basak SC, Gute BD, Mills D: Similarity methods in analog selection, property estimation and clustering of diverse chemicals. ARKIVOC (2006) (ix):157-210.
35. Gute BD, Balasubramanian K, Geiss KT, Basak SC: Prediction of halocarbon toxicity from structure: A hierarchical QSAR approach. Environ Toxicol Pharmacol (2004) 16(1):121-129.
36. Hawkins DM, Basak SC, Kraker JJ, Geiss KT, Witzmann FA: Combining chemodescriptors and biodescriptors in quantitative structure-activity relationship modeling. J Chem Inf Model (2006) 46(1):9-16. • Describes the use of chemodescriptors and biodescriptors in predicting bioactivity.
37. Basak SC, Mills D, Gute BD: Quantitative structure-toxicity relationships using chemodescriptors and biodescriptors. In: Biological Concepts and Techniques in Toxicology: An Integrated Approach. Riviere JE (Ed), Taylor & Francis, New York, NY, USA (2006):61-82.