Graphical representation and mathematical characterization of protein sequences and applications to viral proteins

Advances in Protein Chemistry and Structural Biology

Volumn 83, Issue , 2011, Pages 1-42

  Ghosh, Ambarnil ^a   Nandy, Ashesh ^b  

^a JADAVPUR UNIVERSITY   (India)

^b Centre for Interdisciplinary Research and Education   (India)

Author keywords

avian and swine flu; conserved surface exposed peptides; coronavirus; Graphical representation of proteins; numerical characterisation of proteins; protein characteristics; protein phylogeny; viral proteins and disease

Indexed keywords

EID: 79956122631     PISSN: 18761623     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-381262-9.00001-X     Document Type: Chapter

References (182)

1. G. Aguero-Chapin, A. Antunes, F.M. Ubeira, K.C. Chou, and H. Gonzalez-Diaz Comparative study of topological indices of macro/supramolecular RNA complex networks J. Chem. Inf. Model. 48 2008 2265 2277
2. G. Aguero-Chapin, H. Gonzalez-Diaz, G. de la Riva, E. Rodriguez, A. Sanchez-Rodriguez, and G. Podda MMM-QSAR recognition of ribonucleases without alignment: comparison with an HMM model and isolation from Schizosaccharomyces pombe, prediction, and experimental assay of a new sequence J. Chem. Inf. Model. 48 2008 434 448 (Pubitemid 351473045)
3. G. Aguero-Chapin, H. Gonzalez-Diaz, R. Molina, J. Varona-Santos, E. Uriarte, and Y. Gonzalez-Diaz Novel 2D maps and coupling numbers for protein sequences. The first QSAR study of polygalacturonases; isolation and prediction of a novel sequence from Psidium guajava L FEBS Lett. 580 2006 723 730 (Pubitemid 43152288)
4. G. Aguero-Chapin, J. Varona-Santos, G.A. de la Riva, A. Antunes, T. Gonzalez-Vlla, and E. Uriarte Alignment-free prediction of polygalacturonases with pseudofolding topological indices: experimental isolation from Coffea arabica and prediction of a new sequence J. Proteome Res. 8 2009 2122 2128
5. G.M. Air, and W.G. Laver The neuraminidase of influenza virus Proteins 6 1989 341 356 (Pubitemid 20036940)
6. S.F. Altschul Gap costs for multiple sequence alignment J. Theor. Biol. 138 1989 297 309
7. F. Bai, and T. Wang A 2-D graphical representation of protein sequences based on nucleotide triplet codons Chem. Phys. Lett. 413 2005 458 462 (Pubitemid 41285263)
8. F. Bai, and T. Wang On graphical and numerical representation of protein sequences J. Biomol. Struct. Dyn. 23 2006 537 546
9. F. Bai, W. Zhu, and T. Wang Analysis of similarity between RNA secondary structures Chem. Phys. Lett. 408 2005 258 263 (Pubitemid 40743888)
10. D. Baker, and A. Sali Protein structure prediction and structural genomics Science 294 2001 93 96 (Pubitemid 32952955)
11. J. Baldwin, and C. Chothia Haemoglobin: the structural changes related to ligand binding and its allosteric mechanism J. Mol. Biol. 129 1979 175 220 (Pubitemid 9168805)
12. L.K. Ball, G. Evans, and A. Bostrom Risky business: challenges in vaccine risk communication Pediatrics 101 1998 453 458
13. S.C. Basak, and B.D. Gute Mathematical biodescriptors of proteomics maps: background and applications Curr. Opin. Drug Discov. Devel. 11 2008 320 326 (Pubitemid 351572441)
14. S.C. Basak, D. Mills, B.D. Gute, and R. Natarajan Predicting pharmacological and toxicological activity of heterocyclic compounds using QSAR and molecular modeling S.P. Gupta, QSAR and Molecular Modeling Studies of Heterocyclic Drugs I 2006 Springer-Verlag Berlin-Heidelberg-New York 39 80
15. S.C. Basak, D. Mills, and D.M. Hawkins Characterization of dihydrofolate reductases from multiple strains of Plasmodium falciparum using mathematical descriptors of their inhibitors Chem. Biodivers 8 2011 440 453
16. L.A. Bejarano, and C. Gonzalez Motif trap: a rapid method to clone motifs that can target proteins to defined subcellular localisations J. Cell Sci. 112 Pt 23 1999 4207 4211 (Pubitemid 30122013)
17. H. Berman, K. Henrick, H. Nakamura, and J.L. Markley The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data Nucleic Acids Res. 35 2007 D301 D303
18. N. Blom, T. Sicheritz-Ponten, R. Gupta, S. Gammeltoft, and S. Brunak Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence Proteomics 4 2004 1633 1649 (Pubitemid 38738322)
19. J.B. Chaires Energetics of drug-DNA interactions Biopolymers 44 1997 201 215
20. J.B. Chaires DrugDNA interactions Curr. Opin. Struct. Biol. 8 1998 314 320
21. N.E. Chayen Turning protein crystallisation from an art into a science Curr. Opin. Struct. Biol. 14 2004 577 583 (Pubitemid 39311821)
22. N.E. Chayen High-throughput protein crystallization Adv. Protein. Chem. Struct. Biol. 77 2009 1 22
23. N.E. Chayen, and E. Saridakis Protein crystallization: from purified protein to diffraction-quality crystal Nat Methods 5 2008 147 153 (Pubitemid 351181740)
24. J. Chen, and Y.M. Deng Influenza virus antigenic variation, host antibody production and new approach to control epidemics Virol. J. 6 2009 30
25. M. Chicault, C. Luu Duc, and A. Boucherle Drug protein interactions Arzneimittelforschung 31 1981 1015 1020
26. G. Chikenji, Y. Fujitsuka, and S. Takada Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study Proc. Natl. Acad. Sci. USA 103 2006 3141 3146 (Pubitemid 43346438)
27. K.C. Chou Prediction of protein signal sequences and their cleavage sites Proteins 42 2001 136 139
28. K.C. Chou, and Y.D. Cai Prediction and classification of protein subcellular location-sequence-order effect and pseudo amino acid composition J. Cell. Biochem. 90 2003 1250 1260
29. P.Y. Chou, and G.D. Fasman Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins Biochemistry 13 1974 211 222
30. P.Y. Chou, and G.D. Fasman Prediction of protein conformation Biochemistry 13 1974 222 245
31. J. Colgrove, and R. Bayer Could it happen here? Vaccine risk controversies and the specter of derailment Health Aff. (Millwood) 24 2005 729 739
32. M. Cruz-Monteagudo, H. Gonzalez-Diaz, F. Borges, E.R. Dominguez, and M.N. Cordeiro 3D-MEDNEs: an alternative "in silico" technique for chemical research in toxicology. 2. quantitative proteome-toxicity relationships (QPTR) based on mass spectrum spiral entropy Chem. Res. Toxicol. 21 2008 619 632 (Pubitemid 351498038)
33. M.A. Dea-Ayuela, Y. Perez-Castillo, A. Meneses-Marcel, F.M. Ubeira, F. Bolas-Fernandez, and K.C. Chou HP-Lattice QSAR for dynein proteins: experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence Bioorg. Med. Chem. 16 2008 7770 7776
34. L. Deml, A. Bojak, S. Steck, M. Graf, J. Wild, and R. Schirmbeck Multiple effects of codon usage optimization on expression and immunogenicity of DNA candidate vaccines encoding the human immunodeficiency virus type 1 Gag protein J. Virol. 75 2001 10991 11001 (Pubitemid 33031566)
35. N. Deshpande, K.J. Addess, W.F. Bluhm, J.C. Merino-Ott, W. Townsend-Merino, and Q. Zhang The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema Nucleic Acids Res. 33 2005 D233 D237
36. K.A. Dill, S.B. Ozkan, M.S. Shell, and T.R. Weikl The protein folding problem Annu. Rev. Biophys. 37 2008 289 316
37. K.A. Dill, S.B. Ozkan, T.R. Weikl, J.D. Chodera, and V.A. Voelz The protein folding problem: when will it be solved? Curr. Opin. Struct. Biol. 17 2007 342 346 (Pubitemid 47021366)
38. T. Dingermann Recombinant therapeutic proteins: production platforms and challenges Biotechnol. J. 3 2008 90 97 (Pubitemid 351200935)
39. C.M. Dobson Principles of protein folding, misfolding and aggregation Semin. Cell Dev. Biol. 15 2004 3 16 (Pubitemid 38177363)
40. G.J. Doherty, and H.T. McMahon Mediation, modulation, and consequences of membrane-cytoskeleton interactions Annu. Rev. Biophys. 37 2008 65 95
41. S. Dutta, H.M. Berman, and W.F. Bluhm Using the tools and resources of the RCSB protein data bank Curr. Protoc. Bioinformatics 20 2007 1.9.1 1.9.24
42. S.R. Eddy Hidden Markov models Curr. Opin. Struct. Biol. 6 1996 361 365 (Pubitemid 26197437)
43. D.M. Engelman, T.A. Steitz, and A. Goldman Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins Annu. Rev. Biophys. Biophys. Chem. 15 1986 321 353
44. E. Estrada Characterization of the folding degree of proteins Bioinformatics 18 2002 697 704 (Pubitemid 34679116)
45. E. Estrada, and E. Uriarte Recent advances on the role of topological indices in drug discovery research Curr. Med. Chem. 8 2001 1573 1588 (Pubitemid 33076803)
46. N. Eswar, D. Eramian, B. Webb, M.Y. Shen, and A. Sali Protein structure modeling with MODELLER Methods Mol. Biol. 426 2008 145 159
47. N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M.-y. Shen, U. Pieper, and A. Sali Comparative protein structure modeling using MODELLER Curr. Protoc. Protein Sci. 50 2007 2.9.1 2.9.31
48. G.D. Fasman Protein conformational prediction Trends Biochem. Sci. 14 1989 295 299 (Pubitemid 19187260)
49. H.J. Feldman, and C.W. Hogue Probabilistic sampling of protein conformations: new hope for brute force? Proteins 46 2002 8 23 (Pubitemid 34033572)
50. M. Fernandez, J. Caballero, L. Fernandez, J.I. Abreu, and G. Acosta Classification of conformational stability of protein mutants from 3D pseudo-folding graph representation of protein sequences using support vector machines Proteins 70 2008 167 175 (Pubitemid 350293458)
51. C. Frieden Protein-protein interaction and enzymatic activity Annu. Rev. Biochem. 40 1971 653 696
52. S. Frokjaer, and D.E. Otzen Protein drug stability: a formulation challenge Nat. Rev. Drug Discov. 4 2005 298 306 (Pubitemid 41130943)
53. M.A. Gates A simple way to look at DNA J. Theor. Biol. 119 1986 319 328 (Pubitemid 16123352)
54. J. Geigert Overview of the stability and handling of recombinant protein drugs J. Parenter. Sci. Technol. 43 1989 220 224 (Pubitemid 19248859)
55. A. Ghosh, A. Nandy, and P. Nandy Computational analysis and determination of a highly conserved surface exposed segment in H5N1 avian flu and H1N1 swine flu neuraminidase BMC Struct. Biol. 10 2010 6
56. A. Ghosh, A. Nandy, P. Nandy, B.D. Gute, and S.C. Basak Computational study of dispersion and extent of mutated and duplicated sequences of the H5N1 influenza neuraminidase over the period 19972008 J. Chem. Inf. Model. 49 2009 2627 2638
57. K. Ghosh, S.B. Ozkan, and K.A. Dill The ultimate speed limit to protein folding is conformational searching J. Am. Chem. Soc. 129 2007 11920 11927 (Pubitemid 47515346)
58. A.J. Gibbs, and G.A. McIntyre The diagram, a method for comparing sequences. Its use with amino acid and nucleotide sequences Eur. J. Biochem. 16 1970 1 11
59. H.S. Gold, and R.C. Moellering Jr. Antimicrobial-drug resistance N. Engl. J. Med. 335 1996 1445 1453
60. R.A. Goldsby, T.J. Kindt, and B.A. Osborne Overview of Immune System Kuby Immunology 2000 W.H. Freeman and Company United State of America pp. 3
61. H. Gonzalez-Diaz, Y. Gonzalez-Diaz, L. Santana, F.M. Ubeira, and E. Uriarte Proteomics, networks and connectivity indices Proteomics 8 2008 750 778 (Pubitemid 351362934)
62. H. Gonzalez-Diaz, R. Molina, and E. Uriarte Recognition of stable protein mutants with 3D stochastic average electrostatic potentials FEBS Lett. 579 2005 4297 4301 (Pubitemid 41116355)
63. H. Gonzalez-Diaz, L.G. Perez-Montoto, A. Duardo-Sanchez, E. Paniagua, S. Vazquez-Prieto, and R. Vilas Generalized lattice graphs for 2D-visualization of biological information J. Theor. Biol. 261 2009 136 147
64. H. Gonzalez-Diaz, F. Prado-Prado, and F.M. Ubeira Predicting antimicrobial drugs and targets with the MARCH-INSIDE approach Curr. Top. Med. Chem. 8 2008 1676 1690
65. H. Gonzalez-Diaz, L. Saiz-Urra, R. Molina, Y. Gonzalez-Diaz, and A. Sanchez-Gonzalez Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments J. Comput. Chem. 28 2007 1042 1048 (Pubitemid 46506707)
66. H. Gonzalez-Diaz, S. Vilar, L. Santana, and E. Uriarte Medicinal chemistry and bioinformaticscurrent trends in drugs discovery with networks topological indices Curr. Top. Med. Chem. 7 2007 1015 1029 (Pubitemid 47040529)
67. A.E. Gorbalenya, E.J. Snijder, and W.J. Spaan Severe acute respiratory syndrome coronavirus phylogeny: toward consensus J. Virol. 78 2004 7863 7866 (Pubitemid 38944271)
68. O. Gotoh Optimal alignment between groups of sequences and its application to multiple sequence alignment Comput. Appl. Biosci. 9 1993 361 370 (Pubitemid 23193511)
69. P.R. Gunn, F. Sato, K.F. Powell, A.R. Bellamy, J.R. Napier, and D.R. Harding Rotavirus neutralizing protein VP7: antigenic determinants investigated by sequence analysis and peptide synthesis J. Virol. 54 1985 791 797 (Pubitemid 15014713)
70. S. Gurunathan, D.M. Klinman, and R.A. Seder DNA vaccines: immunology, application, and optimization Annu. Rev. Immunol. 18 2000 927 974 (Pubitemid 30365401)
71. E. Hamori, and J. Ruskin H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences J. Biol. Chem. 258 1983 1318 1327 (Pubitemid 13139379)
72. M. Hatta, P. Gao, P. Halfmann, and Y. Kawaoka Molecular basis for high virulence of Hong Kong H5N1 influenza A viruses Science 293 2001 1840 1842 (Pubitemid 32845783)
73. D.M. Hawkins, S.C. Basak, J. Kraker, K.T. Geiss, and F.A. Witzmann Combining chemodescriptors and biodescriptors in quantitative structure-activity relationship modeling J. Chem. Inf. Model. 46 2006 9 16 (Pubitemid 43282093)
74. H.J. Jeffrey Chaos game representation of gene structure Nucleic Acids Res. 18 1990 2163 2170
75. M. Jiang, and B. Zhu Protein folding on the hexagonal lattice in the HP model J. Bioinform. Comput. Biol. 3 2005 19 34 (Pubitemid 40305482)
76. G. Karp Biological molecules Cell and Molecular Biology 2008 John Wiley & Sons (Asia) Pte Ltd Asia p. 31
77. J.C. Kendrew Structure and function in myoglobin and other proteins Fed. Proc. 18 1959 740 751
78. J.C. Kendrew, G. Bodo, H.M. Dintzis, R.G. Parrish, H. Wyckoff, and D.C. Phillips A three-dimensional model of the myoglobin molecule obtained by x-ray analysis Nature 181 1958 662 666
79. J.C. Kendrew, R.E. Dickerson, B.E. Strandberg, R.G. Hart, D.R. Davies, and D.C. Phillips Structure of myoglobin: A three-dimensional Fourier synthesis at 2 A. resolution Nature 185 1960 422 427
80. A.R. Kinjo, R. Yamashita, and H. Nakamura PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan Database (Oxford) Database published online August 25, 2010) 2010 2010 http://database.oxfordjournals.org/cgi/crossref-forward-links/2010/0/baq021 baq021.
81. J. Koch-Weser, and E.M. Sellers Binding of drugs to serum albumin (first of two parts) N. Engl. J. Med. 294 1976 311 316
82. E.V. Koonin, T.G. Senkevich, and V.V. Dolja The ancient Virus World and evolution of cells Biol. Direct 1 2006 29
83. E.V. Koonin, Y.I. Wolf, K. Nagasaki, and V.V. Dolja The complexity of the virus world Nat. Rev. Microbiol. 7 2009 250
84. L.D. Kramer, J. Li, and P.Y. Shi West Nile virus Lancet Neurol. 6 2007 171 181 (Pubitemid 46099081)
85. D.M. Kristensen, A.R. Mushegian, V.V. Dolja, and E.V. Koonin New dimensions of the virus world discovered through metagenomics Trends Microbiol. 18 2010 11 19
86. S. Kumar, M. Nei, J. Dudley, and K. Tamura MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences Brief Bioinform. 9 2008 299 306 (Pubitemid 351890826)
87. M.M. Lai Coronavirus: organization, replication and expression of genome Annu. Rev. Microbiol. 44 1990 303 333
88. T.T. Lam, C.C. Hon, O.G. Pybus, S.L. Kosakovsky Pond, R.T. Wong, and C.W. Yip Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia PLoS Pathog. 4 2008 e1000130
89. S. Larionov, A. Loskutov, and E. Ryadchenko Chromosome evolution with naked eye: palindromic context of the life origin Chaos 18 2008 013105
90. D.G. Lee, P.I. Kim, Y. Park, E.R. Woo, J.S. Choi, and C.H. Choi Design of novel peptide analogs with potent fungicidal activity, based on PMAP-23 antimicrobial peptide isolated from porcine myeloid Biochem. Biophys. Res. Commun. 293 2002 231 238 (Pubitemid 34694196)
91. T. Lengauer, and R. Zimmer Protein structure prediction methods for drug design Brief. Bioinform. 1 2000 275 288
92. P.M. Leong, and S. Morgenthaler Random walk and gap plots of DNA sequences Comput. Appl. Biosci. 11 1995 503 507
93. Z. Li, M.L. Baker, W. Jiang, M.K. Estes, and B.V. Prasad Rotavirus architecture at subnanometer resolution J. Virol. 83 2009 1754 1766
94. C. Li, and J. Wang New invariant of DNA sequences J. Chem. Inf. Model. 45 2005 115 120 (Pubitemid 40736963)
95. C. Li, L. Xing, and X. Wang 2-D graphical representation of protein sequences and its application to coronavirus phylogeny BMB Rep. 41 2008 217 222 (Pubitemid 351518994)
96. C. Li, X. Yu, L. Yang, X. Zheng, and Z. Wang 3-D maps and coupling numbers for protein sequences Physica A 388 2009 1967 1972
97. B. Liao, Y. Liu, R. Li, and W. Zhu Coronavirus phylogeny based on triplets of nucleic acids bases Chem. Phys. Lett. 421 2006 313 318
98. Y.Z. Liu, and T.M. Wang Vector representations and related matrices of DNA primary sequence based on L-tuple Math. Biosci. 227 2010 147 152
99. F. Locatelli, and L.D. Vecchio Darbepoetin alfa Amgen Curr. Opin. Investig. Drugs 2 2001 1097 1104 (Pubitemid 32780711)
100. J.A. Lopez, A.J. Maldonado, M. Gerder, J. Abanero, J. Murgich, and F.H. Pujol Characterization of neuraminidase-resistant mutants derived from rotavirus porcine strain OSU J. Virol. 79 2005 10369 10375 (Pubitemid 41098577)
101. R.M. MacCallum, A.C. Martin, and J.M. Thornton Antibody-antigen interactions: contact analysis and binding site topography J. Mol. Biol. 262 1996 732 745 (Pubitemid 26343518)
102. L. Makowski, D.J. Rodi, S. Mandava, D.D. Minh, D.B. Gore, and R.F. Fischetti Molecular crowding inhibits intramolecular breathing motions in proteins J. Mol. Biol. 375 2008 529 546 (Pubitemid 350192471)
103. J.L. Markley, E.L. Ulrich, H.M. Berman, K. Henrick, H. Nakamura, and H. Akutsu BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions J. Biomol. NMR 40 2008 153 155
104. K.M. Menne, H. Hermjakob, and R. Apweiler A comparison of signal sequence prediction methods using a test set of signal peptides Bioinformatics 16 2000 741 742
105. M.C. Meyer, and D.E. Guttman The binding of drugs by plasma proteins J. Pharm. Sci. 57 1968 895 918
106. M.P. Morrow, and D.B. Weiner DNA drugs come of age Sci. Am. 303 2010 49 53
107. A. Moscona Oseltamivir-resistant influenza? Lancet 364 2004 733 734 (Pubitemid 39165079)
108. A. Moscona Oseltamivir resistancedisabling our influenza defenses N. Engl. J. Med. 353 2005 2633 2636 (Pubitemid 41817709)
109. A. Moscona Global transmission of oseltamivir-resistant influenza N. Engl. J. Med. 360 2009 953 956
110. D. Mount Bioinformatics, sequence and genome analysis 2nd edn. 2004 Cold Spring Harbor Press Cold Spring Harbor, NY pp. 337
111. C.R. Munteanu, A.L. Magalhaes, E. Uriarte, and H. Gonzalez-Diaz Multi-target QPDR classification model for human breast and colon cancer-related proteins using star graph topological indices J. Theor. Biol. 257 2009 303 311
112. H. Nakamura, N. Ito, and M. Kusunoki Development of PDBj: Advanced database for protein structures Tanpakushitsu Kakusan Koso 47 2002 1097 1101
113. A. Nandy A new graphical representation and analysis of DNA sequence structure: I. methodology and application to globin genes Curr. Sci. 66 1994 309 314
114. A. Nandy Empirical relationship between intra-purine and intra-pyrimidine differences in conserved gene sequences PLoS ONE 4 2009 e6829
115. A. Nandy Towards stable vaccines: Contributions from DNA and protein numerical characterization studies 2010 50th Anniversary Celebration with Mathematical Chemistry, Universidad de Pamplona, Pamplona, Colombia
116. A. Nandy, and S.C. Basak New approaches to drug-DNA interactions based on graphical representation and numerical characterization of DNA sequences Curr. Comput. Aided Drug Des. 6 2010 283 289
117. A. Nandy, S.C. Basak, and B.D. Gute Graphical representation and numerical characterization of H5N1 avian flu neuraminidase gene sequence J. Chem. Inf. Model. 47 2007 945 951 (Pubitemid 46973709)
118. A. Nandy, A. Ghosh, and P. Nandy Numerical characterization of protein sequences and application to voltage-gated sodium channel alpha subunit phylogeny In Silico Biol. 9 2009 77 87
119. A. Nandy, M. Harle, and S.C. Basak Mathematical descriptors of DNA sequences: development and applications ARKIVOC 9 2006 211 238 (Pubitemid 44527394)
120. A. Nandy, and P. Nandy Graphical analysis of DNA sequence structure: II. Relative abundances of nucleotides in DNAs, gene evolution and duplication Curr. Sci. 68 1995 75 85
121. A. Nandy, and P. Nandy On the uniqueness of quantitative DNA difference descriptors in 2D graphical representation models Chem. Phys. Lett. 368 2003 102 107 (Pubitemid 36002836)
122. S.B. Needleman, and C.D. Wunsch A general method applicable to the search for similarities in the amino acid sequence of two proteins J. Mol. Biol. 48 1970 443 453
123. M. Novic, and M. Randic Representation of proteins as walks in 20-D space SAR QSAR Environ. Res. 19 2008 317 337 (Pubitemid 351998858)
124. C.A. Opitz, M. Kulke, M.C. Leake, C. Neagoe, H. Hinssen, and R.J. Hajjar Damped elastic recoil of the titin spring in myofibrils of human myocardium Proc. Natl. Acad. Sci. USA 100 2003 12688 12693 (Pubitemid 37339960)
125. L. Otvos Jr. Peptide-based drug design: here and now Methods Mol. Biol. 494 2008 1 8
126. J. Owens Building blocks for peptide drugs Nat. Rev. Drug Discov. 3 2004 476 (Pubitemid 38807527)
127. A.A. Owoade, N.A. Gerloff, M.F. Ducatez, J.O. Taiwo, J.R. Kremer, and C.P. Muller Replacement of sublineages of avian influenza (H5N1) by reassortments, sub-Saharan Africa Emerg. Infect. Dis. 14 2008 1731 1735
128. C.B. Packhaeuser, J. Schnieders, C.G. Oster, and T. Kissel In situ forming parenteral drug delivery systems: an overview Eur. J. Pharm. Biopharm. 58 2004 445 455 (Pubitemid 39037247)
129. C.K. Peng, S.V. Buldyrev, A.L. Goldberger, S. Havlin, F. Sciortino, and M. Simons Long-range correlations in nucleotide sequences Nature 356 1992 168 170
130. D.N. Perkins, D.J. Pappin, D.M. Creasy, and J.S. Cottrell Probability-based protein identification by searching sequence databases using mass spectrometry data Electrophoresis 20 1999 3551 3567 (Pubitemid 30007252)
131. M.F. Perutz Structure of hemoglobin Brookhaven Symp. Biol. 13 1960 165 183
132. M.F. Perutz, M.G. Rossmann, A.F. Cullis, H. Muirhead, G. Will, and A.C. North Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis Nature 185 1960 416 422
133. M.F. Perutz, and O. Weisz Crystal structure of human carboxyhaemoglobin Nature 160 1947 786
134. B. Peters, J. Sidney, P. Bourne, H.H. Bui, S. Buus, and G. Doh The design and implementation of the immune epitope database and analysis resource Immunogenetics 57 2005 326 336 (Pubitemid 40905051)
135. R.E. Phillips, S. Rowland-Jones, D.F. Nixon, F.M. Gotch, J.P. Edwards, and A.O. Ogunlesi Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition Nature 354 1991 453 459 (Pubitemid 21896855)
136. E.T. Powers, and D.L. Powers Mechanisms of protein fibril formation: nucleated polymerization with competing off-pathway aggregation Biophys. J. 94 2008 379 391
137. G.N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan Stereochemistry of polypeptide chain configurations J. Mol. Biol. 7 1963 95 99
138. G.N. Ramachandran, and V. Sasisekharan Conformation of polypeptides and proteins Adv. Protein Chem. 23 1968 283 438
139. M. Randic Graphical representations of DNA as 2-D map Chem. Phys. Lett. 386 2004 468
140. M. Randic Spectrum-like graphical representation of DNA based on codons Acta Chim. Slov. 53 2006 477 485
141. M. Randic, D. Butina, and J. Zupan Novel 2-D graphical representation of proteins Chem. Phys. Lett. 419 2006 528 532 (Pubitemid 43220524)
142. M. Randic, N. Lers, D. Plavsic, S.C. Basak, and A.T. Balaban Four-color map representation of DNA or RNA sequences and their numerical characterization Chem. Phys. Lett. 407 2005 205 208 (Pubitemid 40584111)
143. M. Randic, M. Novic, and M. Vracko On novel representation of proteins based on amino acid adjacency matrix SAR QSAR Environ. Res. 19 2008 339 349 (Pubitemid 351998857)
144. M. Randic, M. Vracko, N. Lers, and D. Plavsic Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation Chem. Phys. Lett. 371 2003 202
145. M. Randic, M. Vracko, N. Lers, and D. Plavsic Novel 2-D graphical representation of DNA sequences and their numerical characterization Chem. Phys. Lett. 368 2003 1
146. M. Randic, M. Vracko, A. Nandy, and S.C. Basak On 3-D graphical representation of DNA primary sequences and their numerical characterization J. Chem. Inf. Comput. Sci. 40 2000 1235 1244
147. M. Randic, M. Vracko, J. Zupan, and M. Novic Compact 2-D graphical representation of DNA Chem. Phys. Lett. 373 2003 558
148. 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
149. C. Raychaudhury, and A. Nandy Indexing scheme and similarity measures for macromolecular sequences J. Chem. Inf. Comput. Sci. 39 1999 243 247 (Pubitemid 129538910)
150. I. Rayment Kinesin and myosin: molecular motors with similar engines Structure 4 1996 501 504 (Pubitemid 126657543)
151. A.H. Reid, T.G. Fanning, T.A. Janczewski, and J.K. Taubenberger Characterization of the 1918 "Spanish" influenza virus neuraminidase gene Proc. Natl. Acad. Sci. USA 97 2000 6785 6790 (Pubitemid 30412792)
152. J.D. Retief Phylogenetic analysis using PHYLIP Methods Mol. Biol. 132 2000 243 258
153. P. Roach, D. Farrar, and C.C. Perry Interpretation of protein adsorption: surface-induced conformational changes J. Am. Chem. Soc. 127 2005 8168 8173 (Pubitemid 40799673)
154. P. Roach, D. Farrar, and C.C. Perry Surface tailoring for controlled protein adsorption: effect of topography at the nanometer scale and chemistry J. Am. Chem. Soc. 128 2006 3939 3945
155. R.J. Russell, L.F. Haire, D.J. Stevens, P.J. Collins, Y.P. Lin, and G.M. Blackburn The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design Nature 443 2006 45 49 (Pubitemid 44344043)
156. G.B. Ruvkun, and F.M. Ausubel A general method for site-directed mutagenesis in prokaryotes Nature 289 1981 85 88 (Pubitemid 11178462)
157. F. Sanger The arrangement of amino acids in proteins Adv. Protein Chem. 7 1952 1 67
158. F. Sanger, and E.O. Thompson The amino-acid sequence in the glycyl chain of insulin. I. The identification of lower peptides from partial hydrolysates Biochem. J. 53 1953 353 366
159. F. Sanger, and H. Tuppy The amino-acid sequence in the phenylalanyl chain of insulin. I. The identification of lower peptides from partial hydrolysates Biochem. J. 49 1951 463 481
160. H. Schellekens Bioequivalence and the immunogenicity of biopharmaceuticals Nat. Rev. Drug Discov. 1 2002 457 462 (Pubitemid 37361488)
161. H.B. Shen, and K.C. Chou Predicting protein fold pattern with functional domain and sequential evolution information J. Theor. Biol. 256 2009 441 446
162. T.F. Smith, and M.S. Waterman Identification of common molecular subsequences J. Mol. Biol. 147 1981 195 197
163. T.F. Smith, M.S. Waterman, and C. Burks The statistical distribution of nucleic acid similarities Nucleic Acids Res. 13 1985 645 656
164. K. Tamura, J. Dudley, M. Nei, and S. Kumar MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0 Mol. Biol. Evol. 24 2007 1596 1599 (Pubitemid 47236692)
165. S. Tangri, B.R. Mothe, J. Eisenbraun, J. Sidney, S. Southwood, and K. Briggs Rationally engineered therapeutic proteins with reduced immunogenicity J. Immunol. 174 2005 3187 3196 (Pubitemid 40354020)
166. S.J. Teague Implications of protein flexibility for drug discovery Nat. Rev. Drug Discov. 2 2003 527 541 (Pubitemid 37361745)
167. R. Todeschini, D. Ballabio, V. Consonni, and A. Mauri A new similarity/diversity measure for the characterization of DNA sequences Croat. Chem. Acta 81 2008 657 664
168. R. Todeschini, V. Consonni, A. Mauri, and D. Ballabio Characterization of DNA primary sequences by a new similarity/diversity measure based on the partial ordering J. Chem. Inf. Model. 46 2006 1905 1911 (Pubitemid 44625961)
169. N. Tokuriki, C.J. Oldfield, V.N. Uversky, I.N. Berezovsky, and D.S. Tawfik Do viral proteins possess unique biophysical features? Trends Biochem. Sci. 34 2009 53 59
170. J.B. Ulmer, R.R. Deck, A. Yawman, A. Friedman, C. Dewitt, and D. Martinez DNA vaccines for bacteria and viruses Adv. Exp. Med. Biol. 397 1996 49 53 (Pubitemid 26066559)
171. J.B. Ulmer, J.C. Sadoff, and M.A. Liu DNA vaccines Curr. Opin. Immunol. 8 1996 531 536 (Pubitemid 26280783)
172. L. van der Hoek, K. Pyrc, M.F. Jebbink, W. Vermeulen-Oost, R.J. Berkhout, and K.C. Wolthers Identification of a new human coronavirus Nat. Med. 10 2004 368 373 (Pubitemid 38508514)
173. S. Velankar, C. Best, B. Beuth, C.H. Boutselakis, N. Cobley, and A.W. Sousa Da Silva PDBe: Protein Data Bank in Europe Nucleic Acids Res. 38 2010 D308 D317
174. D. Vijaykrishna, L.L. Poon, H.C. Zhu, S.K. Ma, O.T. Li, and C.L. Cheung Reassortment of pandemic H1N1/2009 influenza A virus in swine Science 328 2010 1529
175. S. Vilar, and H. Gonzlez-Daz QSPR models for human Rhinovirus surface networks H. Gonzlez-Daz, C.R. Munteanu, Topological Indices for Medicinal Chemistry, Biology, Parasitology, Neurological and Social Networks 2010 145 161
176. S. Vilar, H. Gonzalez-Diaz, L. Santana, and E. Uriarte QSAR model for alignment-free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP-lattice networks J. Comput. Chem. 29 2008 2613 2622
177. R. Vita, L. Zarebski, J.A. Greenbaum, H. Emami, I. Hoof, and N. Salimi The immune epitope database 2.0 Nucleic Acids Res. 38 2010 D854 D862
178. J. Wang, and W. Wang A computational approach to simplifying the protein folding alphabet Nat. Struct. Biol. 6 1999 1033 1038 (Pubitemid 29519597)
179. I. Wiesner, and D. Wiesnerova 2D random walk representation of Begonia × tuberhybrida multiallelic loci used for germplasm identification Biologia Plantarum 54 2010 353 356
180. W.L. Wu, Y. Chen, P. Wang, W. Song, S.Y. Lau, and J.M. Rayner Antigenic profile of avian H5N1 viruses in Asia from 2002 to 2007 J. Virol. 82 2008 1798 1807 (Pubitemid 351222435)
181. X. Yang, and X. Yu An introduction to epitope prediction methods and software Rev. Med. Virol. 19 2009 77 96
182. S.S. Yau, J. Wang, A. Niknejad, C. Lu, N. Jin, and Y.K. Ho DNA sequence representation without degeneracy Nucleic Acids Res. 31 2003 3078 3080 (Pubitemid 37441767)