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Numerical approach to structure, folding and aggregation of proteins

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In this talk, I briefly review some recent developments in numerical approach to structure, folding and aggregation of proteins. The topics under discussion include: (1) developments of algorithms and computer packages for all-atom simulations of proteins [1], (2) development of algorithm to compute volume V, surface area A, and cavity of proteins by analytic equations [2], (3) unfolding and refolding of immunoglobulin domain I27 and ubiquitin [3], and (4) simple models for relaxation and aggregation of proteins [4,5].

[1] F. Eisenmenger, U. H.E. Hansmann, S. Hayryan, and C.-K. Hu. Computer Phys. Commu. 138, 192-212 (2001) and 174, 422 (2006); C.-Y. Lin, C.-K. Hu, and U.H.E. Hansmann, Proteins 52, 436-445 (2003); S. Hayrian, C.-K. Hu, S.-Y. Hu and R.-J. Shang. J. Comp. Chem. 22, 1287-1296 (2001); R. G. Ghulghazaryan, S. Hayryan and C.-K. Hu. J. Comp. Chem., 28, 715 (2007).

[2] S. Hayryan, C.-K. Hu, J. Skvrivanek, E. Hayrjan, I. Pokorny. J. Comp. Chem. 26, 334 (2005); J. Busa, J. Dzurina, E. Hayryan, S. Hayryan, C.-K. Hu, J. Plavka, I. Pokorny, J. Skrivanek, and M-C. Wu. Comp. Phys. Commun. 165, 59 (2005); J. Busa,, S. Hayryan, C.-K. Hu, J. Skrivanek, and M.-C. Wu, J. Comp. Chem. 30, 346-357 (2009) and Comp. Phys. Commun. 181, 2116 (2010).

[3] M.-S. Li, C.-K. Hu, D. K. Klimov, and D. Thirumalai, Proc. Natl. Acad. Sci. USA 103 , 93 (2006); M.-S. Li, M. Kouza and C.-K. Hu, Biophysical J. 91, 547(2007). M. Kouza, C.-K. Hu and M. S. Li, J. Chem. Phys 128, 045103 (2008).

[4] M. S. Li, N. T. Co, G. Reddy, C. -K. Hu, J. E. Straub, and D. Thirumalai, Phys. Rev. Lett. 105, 218101(2010).

[5] W.-J. Ma and C.-K. Hu, J. Phys. Soc. Japan 79, 024005, 024006, 054001, 104002 (2010); C.-K. Hu and W.-J. Ma, Prog. Theo. Phys. Supp. 184, 369 (2010).

This talk is part of the Irregular seminars in TCM series.

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