Abstract
We develop a novel method for predicting the inter-residue contacts of a protein from evolutionary information obtained from the alignment of multiple sequences. Our method is based on information theory, where we use conditional mutual information so that the spurious correlations coming from indirect effects are removed. The benchmark test shows better performance than the previous method using mutual information does, suggesting the potential of the new method.
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Y. Zhang and J. Skolnick, Proc. Natl. Acad. Sci. USA 101, 7594 (2004).
A. Fiser and A. Sali, Methods Enzymol. 374, 461 (2003).
S. Ovchinnikov, D. E. Kim, R. Y.-R. Wang, Y. Liu, F. DiMaio and D. Baker, Proteins 84 (S1), 67 (2016).
D. S. Marks, L. J. Colwell, R. Sheridan, T. A. Hopf, A. Pagnani, R. Zecchina and C. Sander, PLos One 6, e28766 (2011).
J. I. Sulkowska, F. Morcos, M. Weigt, T. Hwa, and J. N. Onuchic, Proc. Natl. Acad. Sci. USA 109, 10340 (2012).
T. Nugent and D. T. Jones, Proc. Natl. Acad. Sci. USA 109, E1540 (2012).
T. A. Hopf, L. J. Colwell, R. Sheridan, B. Rost, C. Sander and D. S. Marks, Cell 149, 1607 (2012).
U. Göbel, C. Sander, R. Schneider and A. Valencia, Proteins 18, 309 (1994).
S. W. Lockless and R. Ranganathan, Science 286, 295 (1999).
D. K. Chiu and T. Kolodziejczak, Bioinformatics 7, 347 (1991).
S. D. Dunn, L. M.Wahl, and G. B. Gloor, Bioinformatics 24, 333 (2008).
A. A. Fodor and R. W. Aldrich, Proteins 56, 211 (2004).
D. T. Jones, D. W. A. Buchan, D. Cozzetto and M. Pontil, Bioinformatics 28, 184 (2012).
M. Weigt, R. A. White, H. Szurmant, J. A. Hoch and T. Hwa, Proc. Natl. Acad. Sci. USA 106, 67 (2009).
F. Morcos, A. Pagnani, B. Lunt, A. Bertolino, D. S. Marks, C. Sander, R. Zecchina, J. N. Onuchic, T. Hwa and M. Weigt, Proc. Natl. Acad. Sci. USA 108, E1293 (2011).
M. Ekeberg, Cecilia Lövkvist, Y. Lan, M. Weigt and E. Aurell, Phys. Rev. E 87, 012707 (2013).
R. L. Dobrushin, Dokl. Akad. Nauk. 126, 474 (1959).
A. D Wyner, Information and Control 38, 51 (1978).
M. Punta, P. C. Coggill, R. Y. Eberhardt, J. Mistry, J. Tate, C. Boursnell, N. Pang, K. Forslund, G. Ceric, J. Clements, A. Heger, L. Holm, E. L. L. Sonnhammer, S. R. Eddy, A. Bateman and R. D. Finn, Nucleic Acids Res. 40, D290 (2012).
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Byeon, JY., Lee, J. Protein contact prediction by using information theory. Journal of the Korean Physical Society 70, 876–879 (2017). https://doi.org/10.3938/jkps.70.876
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DOI: https://doi.org/10.3938/jkps.70.876