journal article Mar 30, 2012

Balanced and Bias-Corrected Computation of Conformational Entropy Differences for Molecular Trajectories

View at Publisher Save 10.1021/ct200910z
Topics

No keywords indexed for this article. Browse by subject →

References
86
[1]
Jaynes E. T. (1979)
[2]
Ben-Naim A. (2008) 10.1142/6469
[3]
Clausius R. Ann. Phys. (1865) 10.1002/andp.18652010702
[4]
A Mathematical Theory of Communication

C. E. Shannon

Bell System Technical Journal 1948 10.1002/j.1538-7305.1948.tb01338.x
[5]
Salwiczek M. Chem.—Eur. J. (2009) 10.1002/chem.200802136
[6]
Makhatadze G. I. Biophys. Chem. (1994) 10.1016/0301-4622(94)00050-6
[7]
Carlsson J. Phys. Chem. Chem. Phys. (2006) 10.1039/b608486a
[8]
Meirovitch H. Curr. Opin. Struct. Biol. (2007) 10.1016/j.sbi.2007.03.016
[9]
Polyansky A. A. Methods Mol. Biol. (2012) 10.1007/978-1-61779-465-0_21
[10]
Stern O. Ann. Phys. (1916) 10.1002/andp.19163561902
[11]
Schlitter J. Chem. Phys. Lett. (1993) 10.1016/0009-2614(93)89366-p
[12]
Absolute entropies from molecular dynamics simulation trajectories

Heiko Schäfer, Alan E. Mark, Wilfred F. van Gunsteren

The Journal of Chemical Physics 2000 10.1063/1.1309534
[13]
Andricioaei I. J. Chem. Phys. (2001) 10.1063/1.1401821
[14]
Carlsson J. J. Phys. Chem. B (2005) 10.1021/jp046022f
[15]
Harris S. A. J. Phys.: Condens. Matter (2007)
[16]
Rojas O. L. J. Chem. Phys. (1986) 10.1063/1.451296
[17]
Numata J. Genome Inform. (2007)
[18]
Baron R. J. Chem. Theory Comput. (2009) 10.1021/ct900373z
[19]
Hensen U. PLoS One (2010) 10.1371/journal.pone.0009179
[20]
Hyvärinen A. (2001) 10.1002/0471221317
[21]
Matsuda H. Phys. Rev. E (2000) 10.1103/physreve.62.3096
[22]
Noy A. J. Mol. Biol. (2004) 10.1016/j.jmb.2004.07.048
[23]
Essential dynamics of proteins

Andrea Amadei, Antonius B. M. Linssen, Herman J. C. Berendsen

Proteins: Structure, Function, and Bioinformatics 1993 10.1002/prot.340170408
[24]
Mukherjee A. J. Phys. Chem. Lett. (2011) 10.1021/jz2013566
[25]
Chang C.-E. J. Chem. Theory Comput. (2005) 10.1021/ct0500904
[26]
Mendez R. Phys. Rev. Lett. (2010) 10.1103/physrevlett.104.228103
[27]
Method for estimating the configurational entropy of macromolecules

Martin Karplus, Joseph N. Kushick

Macromolecules 1981 10.1021/ma50003a019
[28]
Nola A. D. Macromolecules (1984) 10.1021/ma00140a029
[29]
Harpole K. W. J. Phys. Chem. B (2011) 10.1021/jp111176x
[30]
Darian E. J. Comput. Chem. (2005) 10.1002/jcc.20198
[31]
Wang J. J. Chem. Theory Comput. (2006) 10.1021/ct050118b
[32]
Li D.-W. J. Phys. Chem. B (2007) 10.1021/jp075220e
[33]
Li D. W. Phys. Rev. Lett. (2009) 10.1103/physrevlett.102.118108
[34]
Li D.-W. J. Phys. Chem. B (2010) 10.1021/jp109908u
[35]
Suárez E. J. Chem. Theory Comput. (2011) 10.1021/ct200216n
[36]
Cheluvaraja S. J. Chem. Phys. (2006) 10.1063/1.2208608
[37]
Meirovitch H. J. Mol. Recognit. (2010) 10.1002/jmr.973
[38]
Pearlman, D. A.; Rao, B. G.InEncyclopedia of Computational Chemistry;Schleyer, P v. R., Ed. 1998; Vol.2, pp1036–1061.
[39]
Estimating entropies from molecular dynamics simulations

Christine Peter, Chris Oostenbrink, Arthur van Dorp et al.

The Journal of Chemical Physics 2004 10.1063/1.1636153
[40]
Free Energy Calculations
Springer Series in CHEMICAL PHYSICS 2007 10.1007/978-3-540-38448-9
[41]
Sinai Y. G. Dokl. Akad. Nauk S.S.S.R. (1959)
[42]
Dzugutov M. Phys. Rev. Lett. (1998) 10.1103/physrevlett.81.1762
[43]
Wissman B. D. Phys. Rev. E (2011) 10.1103/physreve.84.046204
[44]
Ceriotti M. Proc. Natl. Acad. Sci. U.S.A (2011) 10.1073/pnas.1108486108
[45]
Brandman R. PLoS One (2012) 10.1371/journal.pone.0029377
[46]
Watanabe H. Chem—Biol. Inf. J. (2010)
[47]
Extraction of configurational entropy from molecular simulations via an expansion approximation

Benjamin J. Killian, Joslyn Yundenfreund Kravitz, Michael K. Gilson

The Journal of Chemical Physics 2007 10.1063/1.2746329
[48]
Killian B. J. J. Mol. Biol. (2009) 10.1016/j.jmb.2009.04.003
[49]
How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

Stefano Piana, Kresten Lindorff-Larsen, David E. Shaw

Biophysical Journal 2011 10.1016/j.bpj.2011.03.051
[50]
Pitzer K. S. J. Chem. Phys. (1946) 10.1063/1.1932193

Showing 50 of 86 references

Metrics
30
Citations
86
References
Details
Published
Mar 30, 2012
Vol/Issue
8(4)
Pages
1235-1245
Cite This Article
Jorge Numata, Ernst-Walter Knapp (2012). Balanced and Bias-Corrected Computation of Conformational Entropy Differences for Molecular Trajectories. Journal of Chemical Theory and Computation, 8(4), 1235-1245. https://doi.org/10.1021/ct200910z