АЛГОРИТМ ПРЕДСКАЗАНИЯ ВЗАИМОДЕЙСТВИЯ БЕЛКОВ НА ОСНОВЕ СТРУКТУРНОЙ ГОМОЛОГИИ
Abstract
Предлагается оригинальный алгоритм предсказания взаимодействия белков, основанный на
структурной схожести с экспериментально определенным интерфейсом белкового комплекса, отобранным из базы интерфейсов белковых комплексов. Пара свободных белков выравнивается на интерфейс из библиотеки белок-белковых интерфейсов. Выравнивание выполняется с помощью метода динамического программирования путем максимизации корреляции между матрицами расстояний отрезков интерфейса и белка.
About the Authors
Т. Кирис
Объединенный институт проблем информатики НАН Беларуси
Belarus
Belarus
А. Тузиков
Объединенный институт проблем информатики НАН Беларуси
Belarus
Belarus
References
1. Tramontano, A. The Ten Most Wanted Solutions in Protein Bioinformatics /
2. A. Tramontano. - Boca Raton : Chapman and Hall/CRC, 2005. - 216 p.
3. Lensink, M.F. Docking and scoring protein interactions: CAPRI 2009 / M.F. Lensink,
4. S.J. Wodak // Proteins. - 2010. - Vol. 78, № 15. - P. 3073-3084.
5. The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI / K. Wiehe [et al.] //
6. Proteins. - 2007. - Vol. 69. - P. 719-725.
7. Schneidman-Duhovny, D. Automatic prediction of protein interactions with large scale motion / D. Schneidman-Duhovny, R. Nussinov, H. Wolfson // Proteins. - 2007. - Vol. 69. - P. 764-773.
8. PIPER: an FFT-based protein docking program with pairwise potentials / D. Kovakov
9. [et al.] // Proteins. - 2006. - Vol. 65. - P. 392-406.
10. Kowalsman, N. Inherent limitations in protein-protein docking procedures / N. Kowalsman, M. Eisenstein // Bioinformatics. - 2007. - Vol. 23. - P. 421-426.
11. Lu, L. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions
12. by multimeric threading / L. Lu, H. Lu, J. Skolnick // Proteins. - 2002. - Vol. 49. - P. 350-364.
13. Kundrotas, P.J. Predicting 3d structures of transient protein_protein complexes by homology / P.J. Kundrotas, E. Alexov // Biochimica et Biophysica Acta. - 2006. - Vol. 1764. - P. 1498-1511.
14. Fast and accurate modeling of protein-protein interactions by combining template-interfacebased docking with flexible refinement / N. Tuncbag [et al.] // Proteins. - 2012. - Vol. 80. - P. 1239 - 1249.
15. A structural perspective on protein-protein interactions / R. Russel [et al.] // Curr Opin
16. Struct Biol. - 2004. - Vol. 14. - P. 313-324.
17. Sinha, R. Docking by structural similarity at protein-protein interfaces / R. Sinha,
18. P. Kundrotas, I. Vakser // Proteins. - 2010. - Vol. 78. - P. 3235-3241.
19. Vreven, T. Integrating atom-based and residue-based scoring functions for protein-protein docking / T. Vreven, H. Hwang, Z. Weng // Protein Science. - 2011. - Vol. 20. - P. 1576-1586.
20. Protein-protein docking with simultaneous optimization of rigid-body displacement and
21. side-chain conformations / J.J. Gray [et al.] // J. Mol. Biol. - 2003. - Vol. 331, № 1. - P. 281-299.
22. FireDock: a web server for fast interaction re-nement in molecular docking / E. Maschiach
23. [et al.] // Nucleic Acids Res. - 2008. - Vol. 36. - P. W229-W232.
24. Fernandez-Recio, J. ICM-DISCO docking by global energy minimization with fully flexible
25. side-chains / J. Fernandez-Recio, M. Totrov, R. Abagyan // Proteins. - 2003. - Vol. 52. - P. 113-117.
26. Dominguez, C. HADDOCK: a protein-protein docking approach based on biochemical
27. and/or biophysical information / C. Dominguez, R. Boelens, A. Bonvin // J. Am. Chem. Soc. - 2003. - Vol. 125. - P. 1731-1737.
28. Kozakov, D. Discrimination of near-native structures in protein-protein docking by testing the stability of local minima / D. Kozakov, O. Schueler-Furman, S. Vajda // Proteins. - 2008. - Vol. 72. - P. 993-1004.
29. Pierce, B. A combination of rescoring and refinement significantly improves protein
30. docking performance / B. Pierce, Z. Weng // Proteins. - 2008. - Vol. 72. - P. 270-279.
31. Lorenzen, S. Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization / S. Lorenzen, Y. Zhang // Proteins. - 2007. - Vol. 16. - P. 2716-2725.
32. Cavasotto, C. Representing receptor flexibility in ligand docking through relevant normal modes / C. Cavasotto, J. Kovacs, R. Abagyan // J. Am. Chem. Soc. - 2005.- Vol. 127. - P. 9632-9640.
33. Fiorucci, S. Binding site prediction and improved scoring during flexible protein-protein
34. docking with ATTRACT / S. Fiorucci, M. Zacharias // Proteins. - 2010. - Vol. 78. - P. 3131-3139.
35. Kastritis, P. Are scoring functions in protein-protein docking ready to predict interactomes? Clues from a novel binding affinity benchmark / P. Kastritis, A. Bonvin // J. Proteome Res. - 2010. - Vol. 9. - P. 2216-2225.
36. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes / C. Zhang [et al.] // J. Med. Chem. - 2005. - Vol. 48. - P. 2325-2335.
37. Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): A new efficient potential for protein-protein docking / C. Pons [et al.] // J. Chem. Inf. Model. - 2011. - Vol. 51. - P. 370-377.
38. Shen, M. Statistical potential for assessment and prediction of protein structures / M. Shen, A. Sali // Protein Science. - 2006. - Vol. 15. - P. 2507-2524.
39. Liu, S. DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking / S. Liu, I. Vakser // BMC Bioinformatics. - 2011. - Vol. 12. - P. 280-286.
40. Pierce, B. ZRANK: Reranking protein docking predictions with an optimized energy function / B. Pierce, Z. Weng // PROTEINS: Structure, Function, and Bioinformatics. - 2007. - Vol. 67. - P. 1078-1086.
41. Betts, M. An analysis of conformational changes on protein-protein association: implications for predictive docking / M. Betts, M. Sternberg // Protein Eng. - 1999. - Vol. 12. - P. 271-289.
42. Zacharias, M. Accounting for conformational changes during protein-protein docking /
43. M. Zacharias // Curr Opin Struct Biol. - 2010. - Vol. 20, № 2. - P. 180-186.
44. Ding, F. Rapid flexible docking using a stochastic rotamer library of ligands / F. Ding,
45. S. Yin, N.V. Dokholyan // J. Chem. Inf. Model. - 2010. - Vol. 50, № 9. - P. 1623-1632.
46. Principles of flexible protein-protein docking / N. Andrusier [et al.] // Proteins. - 2008. -
47. Vol. 73, № 2. - P. 271-289.
48. Zhang, Y. Scoring function for automated assessment of protein structure template quality / Y. Zhang, J. Skolnick // Proteins. - 2004. - Vol. 57. - P. 702-710.
49. Dockground system of databases for protein recognition studies: Unbound structures for docking / Y. Gao [et al.] // Proteins. - 2007. - Vol. 69, № 4. - P. 845-851.
50. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures /
51. R. Menndez [et al.] // Proteins. - 2005. - Vol. 60. - P. 150-169.
52. Kolodny, R. Approximate protein structural alignment in polynomial time / R. Kolodny,
53. N. Linial // PNAS. - 2004. - Vol. 101. - P. 12201-12206.
54. Kabsch, W.A. A solution for the best rotation to relate two sets of vectors / W.A. Kabsch // Acta Cryst. - 1976. - Vol. 32. - P. 922-923.
55. Horn, R. Matrix Analysis / R. Horn, C. Johnson. - Cambridge University Press, 1985.
56. Protein-protein docking benchmark 2.0: an update / J. Mintseris [et al.] // Proteins. - 2005. - Vol. 60. - P. 214-216.
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ISSN 2617-6963 (Online)
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