Skip to main content

News about Scitation

In December 2016 Scitation will launch with a new design, enhanced navigation and a much improved user experience.

To ensure a smooth transition, from today, we are temporarily stopping new account registration and single article purchases. If you already have an account you can continue to use the site as normal.

For help or more information please visit our FAQs.

banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
The full text of this article is not currently available.
/content/aip/journal/jcp/135/14/10.1063/1.3641894
1.
1. K. Fukuzawa, K. Kitaura, M. Uebayasi, K. Nakata, T. Kaminuma, and T. Nakano, J. Comput. Chem. 26(1), 1 (2005).
http://dx.doi.org/10.1002/jcc.20130
2.
2. X. H. Chen and J. Z. H. Zhang, J. Chem. Phys. 125, 044903 (2006).
http://dx.doi.org/10.1063/1.2218341
3.
3. W. Yang and T.-S. Lee, J. Chem. Phys. 103, 5674 (1995).
http://dx.doi.org/10.1063/1.470549
4.
4. S. L. Dixon and K. M. Merz Jr., in Encyclopedia of Computational Chemistry, edited by P. v. R. Schleyer (Wiley & Sons Ltd, Baffins Lane, Chichester, 1998), Vol. 1, p. 762.
5.
5. X. He and K. M. Merz, J. Chem. Theory Comput. 6(2), 405 (2010).
http://dx.doi.org/10.1021/ct9006635
6.
6. K. A. Dill, J Biol. Chem. 272(2), 701 (1997).
http://dx.doi.org/10.1074/jbc.272.2.701
7.
7. K. M. Merz, J Chem. Theory Comput. 6(5), 1769 (2010).
http://dx.doi.org/10.1021/ct100102q
8.
8. J. C. Faver, M. L. Benson, X. He, B. P. Roberts, B. Wang, M. S. Marshall, M. R. Kennedy, D. C. Sherrill, and K. M. Merz, J. Chem. Theory Comput. 7(3), 790 (2011).
http://dx.doi.org/10.1021/ct100563b
9.
9. J. C. Faver, M. L. Benson, X. He, B. P. Roberts, B. Wang, M. S. Marshall, D. C. Sherrill, and K. M. Merz, PloS ONE 6(4), e18868 (2011).
http://dx.doi.org/10.1371/journal.pone.0018868
10.
10. S. F. Boys and F. Bernardi, Mol. Phys. 19(4), 553 (1970).
http://dx.doi.org/10.1080/00268977000101561
11.
11. D. Moran, A. C. Simmonett, F. E. Leach, W. D. Allen, P. V. Schleyer, and H. F. Schaefer, J. Am. Chem. Soc. 128(29), 9342 (2006).
http://dx.doi.org/10.1021/ja0630285
12.
12. D. Asturiol, M. Duran, and P. Salvador, J. Chem. Phys. 128, 144108 (2008).
http://dx.doi.org/10.1063/1.2902974
13.
13. R. M. Balabin, J. Chem. Phys. 132, 231101 (2010).
http://dx.doi.org/10.1063/1.3442466
14.
14. F. Jensen, J. Chem. Theory Comput. 6(1), 100 (2010).
http://dx.doi.org/10.1021/ct900436f
15.
15. M. N. Ucisik, D. S. Dashti, J. C. Faver, and K. M. Merz, J. Chem. Phys. 135, 085101 (2011).
http://dx.doi.org/10.1063/1.3624750
16.
16. J. M. Word, S. C. Lovell, J. S. Richardson, and D. C. Richardson, J. Mol. Biol. 285(4), 1735 (1999).
http://dx.doi.org/10.1006/jmbi.1998.2401
17.
17. V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling, Proteins 65(3), 712 (2006).
http://dx.doi.org/10.1002/prot.21123
18.
18. D. A. Case, T. A. Darden, I. T. E. Cheatham, C. L. Simmerling, J. Wang, R. R. E. Duke, and R. C. W. Luo, AMBER 11, University of California, San Francisco, 2010.
19.
19. M. J. Frisch, G. W. Trucks, H. B. Schlegel et al., GAUSSIAN 03, Revision E.01, Gaussian, Inc., Wallingford, CT, 2004.
20.
20. X. He, L. Fusti-Molnar, G. L. Cui, and K. M. Merz, J. Phys. Chem. B 113(15), 5290 (2009).
http://dx.doi.org/10.1021/jp8106952
21.
21. See supplementary material at http://dx.doi.org/10.1063/1.3641894 for a description of the molecular fragmentation algorithm used in this study. [Supplementary Material]
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/14/10.1063/1.3641894
Loading
/content/aip/journal/jcp/135/14/10.1063/1.3641894
Loading

Data & Media loading...

Loading

Article metrics loading...

/content/aip/journal/jcp/135/14/10.1063/1.3641894
2011-10-12
2016-12-07

Abstract

Basis set superposition error (BSSE) is a significant contributor to errors in quantum-based energy functions, especially for large chemical systems with many molecular contacts such as folded proteins and protein-ligand complexes. While the counterpoise method has become a standard procedure for correcting intermolecular BSSE, most current approaches to correcting intramolecular BSSE are simply fragment-based analogues of the counterpoise method which require many (two times the number of fragments) additional quantum calculations in their application. We propose that magnitudes of both forms of BSSE can be quickly estimated by dividing a system into interacting fragments, estimating each fragment's contribution to the overall BSSE with a simple statistical model, and then propagating these errors throughout the entire system. Such a method requires no additional quantum calculations, but rather only an analysis of the system's interacting fragments. The method is described herein and is applied to a protein-ligand system, a small helical protein, and a set of native and decoy protein folds.

Loading

Full text loading...

/deliver/fulltext/aip/journal/jcp/135/14/1.3641894.html;jsessionid=tZpjxANimPhaKe3EVyQ2lI9r.x-aip-live-03?itemId=/content/aip/journal/jcp/135/14/10.1063/1.3641894&mimeType=html&fmt=ahah&containerItemId=content/aip/journal/jcp
true
true

Access Key

  • FFree Content
  • OAOpen Access Content
  • SSubscribed Content
  • TFree Trial Content
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
/content/realmedia?fmt=ahah&adPositionList=
&advertTargetUrl=//oascentral.aip.org/RealMedia/ads/&sitePageValue=jcp.aip.org/135/14/10.1063/1.3641894&pageURL=http://scitation.aip.org/content/aip/journal/jcp/135/14/10.1063/1.3641894'
Right1,Right2,Right3,