Uncover the conserved property underlying sequence-distant and structure-similar proteins

Biopolymers

Volumn 93, Issue 4, 2010, Pages 340-347

  Gao, Jun ^a,b   Li Zhijun, Z ^a,c  

^a UNIVERSITY OF THE SCIENCES   (United States)

^b SHANDONG UNIVERSITY   (China)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Average number of interactions; Conservation; Homology modeling; Inter residue interaction

Indexed keywords

CONSERVATION; HYDROGEN BONDS; POTENTIAL ENERGY;

AVERAGE NUMBERS; COMPUTATIONAL TOOLS; HOMOLOGOUS STRUCTURES; HOMOLOGY MODELING; HYDROGEN BONDING INTERACTIONS; INTER-RESIDUE INTERACTIONS; PROTEIN STRUCTURE PREDICTION; SEQUENCE IDENTITY;

PROTEINS;

AMINO ACID SEQUENCE; ARTICLE; HYDROGEN BOND; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

EID: 77949896722     PISSN: 00063525     EISSN: 10970282     Source Type: Journal    
DOI: 10.1002/bip.21342     Document Type: Article

References (26)

1. Gibrat, J. F.; Madej, T.; Bryant, S. H. Curr Opin Struct Biol 1996, 6, 377-385.
2. Anfinsen, C. B. Science 1973, 181, 223-230.
3. Sippl, M. J. Curr Opin Struct Biol 2009, 19, 312-320.
4. Banaszak, L.; Winter, N.; Xu, Z.; Bernlohr, D. A.; Cowan, S.; Jones, T. A. Adv Protein Chem 1994, 45, 89-151.
5. Russell, R. B.; Barton, G. J. J Mol Biol 1994, 244, 332-350.
6. Kinjo, A. R.; Nishikawa, K. Bioinformatics 2004, 20, 2504-2508.
7. Krissinel, E. Bioinformatics 2007, 23, 717-723.
8. Socolich, M.; Lockless, S. W.; Russ, W. P.; Lee, H.; Gardner, K. H.; Ranganathan, R. Nature 2005, 437, 512-518.
9. Kinjo, A. R.; Nakamura, H. PLoS One 2008, 3, e1963.
10. Gromiha, M. M.; Selvaraj, S. Prog Biophys Mol Biol 2004, 86, 235-277.
11. Kauzmann, W. Adv Protein Chem 1959, 14, 1-63.
12. Gao, J.; Bosco, D. A.; Powers, E. T.; Kelly, J. W. Nat Struct Mol Biol 2009, 16, 684-690.
13. Betz, S. F. Protein Sci 1993, 2, 1551-1558.
14. Waldburger, C. D.; Schildbach, J. F.; Sauer, R. T. Nat Struct Biol 1995, 2, 122-128.
15. Gao, J.; Li, Z. J Comput Aided Mol Des DOI 10.1007/s10822-00-9220-.
16. Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. J Mol Biol 1995, 247, 536-540.
17. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res 2000, 28, 235-242.
18. Redfern, O. C.; Harrison, A.; Dallman, T.; Pearl, F. M.; Orengo, C. A. PLoS Comput Biol 2007, 3, e232.
19. Livingstone, C. D.; Barton, G. J. Comput Appl Biosci 1993, 9, 745-756.
20. Case, D. A.; Darden, T. A.; Cheatham, I. T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B. Pearlman, D. A. Amber8; University of California: San Francisco, 2004.
21. McDonald, I. K.; Thornton, J. M. J Mol Biol 1994, 238, 777-793.
22. Sali, A.; Blundell, T. L. J Mol Biol 1993, 234, 779-815.
23. Zhang, Y.; Skolnick, J. Nucleic Acids Res 2005, 33, 2302-2309.
24. Muppirala, U. K.; Li, Z. Protein Eng Des Sel 2006, 19, 265-275.
25. Lobley, A.; Sadowski, M. I.; Jones, D. T. Bioinformatics 2009, 25, 1761-1767.
26. Sali, A.; Potterton, L.; Yuan, F.; van Vlijmen, H.; Karplus, M. Proteins 1995, 23, 318-326.