Geometric similarity between protein-RNA interfaces

Journal of Computational Chemistry

Volumn 30, Issue 16, 2009, Pages 2738-2751

  Zou, Peng ^a,b   Zhou, Jianwei ^b   Tian, Feifei ^c   Shang, Zhicai ^a  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c CHONGQING UNIVERSITY   (China)

Author keywords

Clustering tree; Geometric similarity; Protein RNA interface; RNA recognition theme

Indexed keywords

CLUSTERING TREE; CLUSTERING TREES; DATA SETS; DRUG DESIGN; GEOMETRIC SIMILARITY; HIER-ARCHICAL CLUSTERING; INTERFACE GEOMETRY; MATRIX; NUCLEOTIDE PAIRS; PROTEIN DATA BANK; PROTEIN FAMILY; PROTEIN-RNA INTERACTION; RNA INTERFACE; RNA RECOGNITION; RNA RECOGNITION THEME; SIMILARITY SCORES; SPATIAL RELATIONSHIPS; STRUCTURAL CLASS; TYPE II;

AMINES; AMINO ACIDS; DRUG INTERACTIONS; GEOMETRY; LAWS AND LEGISLATION; ORGANIC ACIDS; RNA;

NUCLEIC ACIDS;

PROTEIN; PUM1 PROTEIN, HUMAN; RNA; RNA BINDING PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; HUMAN; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION;

HUMANS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; RNA; RNA-BINDING PROTEINS;

EID: 70349934526     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21300     Document Type: Article

References (56)

1. Glisovic, T.; Bachorik, J.; Yong, J.; Dreyfuss, G. FEBS Lett 1977, 2008, 582.
2. Ellis, J. J.; Broom, M.; Jones, S. Proteins 2007, 66, 903.
3. Ban, N.; Nissen, P.; Hansen, J.; Moore, P. B.; Steitz, T. A. Science 2000, 289, 905.
4. Wimberly, B. T.; Brodersen, D. E.; Clemons, W. M.; Morgan-Warren, R. J.; Carter, A. P.; Vonrhein, C.; Hartsch, T.; Ramakrishnan, V. Nature 2000, 407, 327.
5. Kim, H.; Jeong, E.; Lee, S. W.; Han, K. FEBS Lett 2003, 552, 231.
6. Morozova, N.; Allers, J.; Myers, J.; Shamoo, Y. Bioinformatics 2006, 22, 2746.
7. Jones, S.; Daley, D.; Luscombe, N.; Berman, H.; Thornton, J. Nucleic Acids Res 2001, 29, 943.
8. Treger, M.; Westhof, E. J Mol Recognit 2001, 14, 199.
9. Jeong, E.; Kim, H.; Lee, S.W.; Han, K. Mol Cells 2003, 16, 161.
10. Kim, O. T. P.; Yura, K.; Go, N. Nucleic Acids Res 2006, 34, 6450.
11. Luscombe, N. M.; Laskowski, R. A.; Thornton, J. M. Nucleic Acids Res 1997, 25, 4940.
12. Zhang, H.; Zhang, J.; Yu, X.; Lu, X.; Zhang, Q.; Jakana, J.; Chen, D. H.; Zhang, X.; Zhou, Z. H. J Virol 1999, 73, 1624.
13. Allers, J.; Shamoo, Y. J Mol Biol 2001, 311, 75.
14. Han, K.; Nepal, C. FEBS Lett 2007, 581, 1881.
15. Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J. Nucleic Acids Res 2009, 37, D369.
16. Shulman-Peleg, A.; Shatsky, M.; Nussinov, R.; Wolfson, H. J. J Mol Biol 2008, 379, 299.
17. Ofran, Y.; Rost, B. J Mol Biol 2003, 325, 377.
18. Chakrabarti, P.; Janin, J. Proteins 2002, 47, 334.
19. Bahadur, R. P.; Chakrabarti, P.; Rodier, F.; Janin, J. J Mol Biol 2004, 336, 943.
20. Saha, S.; Bhattacharyya, R.; Chakrabarti, P. Proteins 2007, 67, 84.
21. Jones, S.; van Heyningen, P.; Berman, H. M.; Thornton, J. M. J Mol Biol 1999, 287, 877.
22. Luscombe, N. M.; Laskowski, R. A.; Thornton, J. M. Nucleic Acids Res 2001, 29, 2860.
23. Selvaraj, S.; Kono, H.; Sarai, A. J Mol Biol 2002, 322, 907.
24. Tsuchiya, Y.; Kinoshita, K.; Nakamura, H. Genome Inform 2002, 13, 310.
25. Lawrence, M. C.; Colman, P. M. J Mol Biol 1993, 234, 946.
26. Chen, R.; Weng, Z. Proteins 2003, 51, 397.
27. Grünberg, R.; Leckner, J.; Nilges, M. Structure 2004, 12, 2125.
28. Falk, K.; Rötzschke, O.; Stefanovic, S.; Jung, G.; Rammensee, H. G. Nature 1991, 351, 290.
29. Keskin, O.; Ma, B.; Nussinov, R. J Mol Biol 2005, 345, 1281.
30. Nussinov, R.; Wolfson, H. J. Proc Natl Acad Sci USA 1991, 88, 10495.
31. Tsai, C. J.; Lin, S. L.; Wolfson, H. J.; Nussinov, R. J Mol Biol 1996, 260, 604.
32. Keskin, O.; Tsai, C. J.; Wolfson, H.; Nussinov, R. Protein Sci 2004, 13, 1043.
33. Kim, W. K.; Henschel, A.; Winter, C.; Schroeder, M. PLoS Comput Biol 2006, 2, 1151.
34. Kono, H.; Sarai, A. Proteins 1999, 35, 114.
35. Gendron, P.; Lemieux, S.; Major, F. J Mol Biol 2001 308 919
36. Pabo, C. O.; Nekludova, L. J Mol Biol 2000, 301, 597.
37. Siggers, T. W.; Silkov, A.; Honig, B. J Mol Biol 2005, 345, 1027.
38. Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. J Mol Biol 1995, 247, 536.
39. Keskin, O.; Nussinov, R. Protein Eng Des Sel 2005, 18, 11.
40. Keskin, O.; Nussinov, R. Structure 2007, 15, 341.
41. Keskin, O.; Gursoy, A.; Ma, B.; Nussinov, R. Chem Rev 2008, 108, 1225.
42. Fischer, T. B.; Holme, J. B.; Miller, I. R.; Parsons, J. R.; Tung, L.; Hu, J. C.; Tsai, J. J Struct Biol 2006, 153, 103.
43. Richardson, D. C.; Richardson, J. S. Protein Sci 1992, 1, 3.
44. Word, J. M.; Lovell, S. C.; Richardson, J. S.; Richardson, D. C. J Mol Biol 1999, 285, 1735.
45. McDonald, I. K.; Thornton, J. M. J Mol Biol 1994, 238, 777.
46. Word, J. M.; Lovell, S. C.; LaBean, T. H.; Taylor, H. C.; Zalis, M. E.; Presley, B. K.; Richardson, J. S.; Richardson, D. C. J Mol Biol 1999, 285, 1711.
47. DeLano, W. L. The PyMOL Molecular Graphics System; DeLano Scientific: San Carlos, CA, USA, 2002.
48. Smith, T. F.; Waterman, M. S. J Mol Bol 1981, 147, 195.
49. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577.
50. Phipps, K. R.; Li, H. Proteins 2007, 67, 121.
51. Canutescu, A. A.; Shelenkov, A. A.; Dunbrack, R. L. Protein Sci 2001, 2003, 12.
52. Gordon, A. E. Classification: Methods for the Exploratory Analysis of Multivariate Data; Chapman and Hall: New York, 1981.
53. Humphrey, W.; Dalke, A.; Schulten, K. J Mol Graphics 1996, 14, 33.
54. Draper, D. E. J Mol Biol 1999, 293, 255.
55. Chao, J. A.; Lee, J. H.; Chapados, B. R.; Debler, E. W.; Schneemann, A.; Williamson, J. R. Nat Struct Mol Biol 2005, 12, 952.
56. Zamyatkin, D. F.; Parra, F.; Alonso, J. M.; Harki, D. A.; Peterson, B. R.; Grochulski, P.; Kenneth, K. S. J Biol Chem 2008, 283, 7705.