Analysis of protein folds using protein contact networks

Pramana - Journal of Physics

Volumn 71, Issue 2, 2008, Pages 369-378

  Barah, Pankaj ^a   Sinha, Somdatta ^a  

^a CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

Contact map; EF hand; Fold recognition; Network; Protein structure; Ubiquitin like

Indexed keywords

ACIDS; AMINATION; AMINES; AMINO ACIDS; FLOW INTERACTIONS; MAPS; MOLECULAR BIOLOGY; ORGANIC ACIDS; PROTEINS; THREE DIMENSIONAL; TOPOLOGY;

AMINO ACID RESIDUES; BIOCHEMICAL FUNCTIONS; COARSE-GRAINED; CONTACT MAP; CONTACT MAPS; CONTACT NETWORKS; CONTACT PATTERNS; EF-HAND; FOLD RECOGNITION; FOLDING MECHANISMS; FUNCTIONAL ROLES; GRAPH-THEORETICAL APPROACH; INTER-ATOMIC INTERACTION; LINEAR CHAINS; LIVING SYSTEMS; LONG-RANGE INTERACTIONS; NATIVE-STATE PROTEIN; NETWORK; NETWORK REPRESENTATIONS; PROTEIN STRUCTURE; PROTEIN STRUCTURES; SECONDARY STRUCTURES; STRUCTURAL ELEMENTS; THREE-DIMENSIONAL SHAPES; UBIQUITIN; UBIQUITIN-LIKE;

PROTEIN FOLDING;

EID: 49749137012     PISSN: 03044289     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12043-008-0170-5     Document Type: Article

References (30)

1. L H Greene and V A Higman, J. Mol. Biol. 334, 781 (2003)
2. N Kannan and S Vishveshwara, J. Mol. Biol. 292, 441 (1999)
3. K V Brinda and S Vishveshwara, Biophys. J. 89, 4159 (2005)
4. K V Brinda and S Vishveshwara, Biophys. J. 92, 2523 (2007)
5. Md. Aftabuddina and S Kundu, Physica A396, 896 (2006)
6. M Vendruscolo, N V Dokholyan, E Paci and M Karplus, Phys. Rev. E65, 061910 (2002)
7. U K Muppirala and Zhijun Li, Protein Engineering, Design & Selection 19, 265 (2006)
8. G Bagler and Somdatta Sinha, Physica A346, 27 (2005)
9. G Bagler and Somdatta Sinha, Bioinformatics 23, 1760 (2007)
10. N S Shiju Lal and Somdatta Sinha, Proceedings of the 11th ADNAT Convention on Advances in Structural Biology and Structure Prediction 134 (2007)
11. Murzin et al, J. Mol. Biol. 247, 536 (1995)
12. G Pollastri and P Baldi, Bioinformatics 18, S62 (2002)
13. D R Westhead, D C Hatton and J M Thornton, Trends in Biochem. Sci. 23, 35 (1998)
14. A Godzik, J Skolnick and A Kolinski, J. Mol. Biol. 227, 227 (1999)
15. J Selbig and P Argos, Proteins: Struct. Funct. Genet. 31, 172 (1998)
16. A M Lesk, L L Conte and T J P Hubbard, Proteins 45(S5), 98 (2001)
17. A R Ortiz, A Kolinski, P Rotkiewiez and J Skolnick, Proteins Suppl. 3, 177 (1999)
18. Bernstein et al, J. Mol. Biol. 112, 535 (1977)
19. H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov and P E Bourne, Nucleic Acids Res. 28, 235 (2000)
20. W L DeLano, The PyMOL Molecular Graphics System (2002), www.pymol.org
21. The MathWorks, Inc. (www.mathworks.com/)
22. V Batagelj and A Mrvar, in Graph drawing software edited by M Jünger and P Mutzel (Springer, Berlin, 2003) p. 77
23. C Rao-Naik, W delaCruz, J M Laplaza, S Tan, J Callis and A J Fisher, J. Biol. Chem. 273, 34976 (1998)
24. A Buchberger, M J Howard, M Proctor and M Bycroft, J. Mol. Biol. 307, 17 (2001)
25. W Gronwald, F Huber, P Grunewald, M Sporner, S Wohlgemuth, C Herrmann and H R Kalbitzer, Structure 9, 1029 (2001)
26. J L Enmon, T de Beer and M Overduin, Biochemistry 39, 4309 (2000)
27. S Kim, D N Cullis, L A Feig and J D Baleja, Biochemistry 40, 6776 (2001)
28. M Andersson, A Malmendal, S Linse, I Ivarsson, S Forsen and L A Svensson, Protein Sci., 6, 1139 (1997)
29. J P Declercq, C Evrard, V Lamzin and J Parello, Protein Sci. 8, 2194 (1999)
30. S Nakayama, N D Moncrief and R H Kretsinger, J. Mol. Evol. 34, 416 (1992)