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Nucleic Acids Research Advance Access published online on May 7, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm328
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts

Mark V. Berjanskii1 and David S. Wishart1,2,3,*

1Department of Computing Science and 2Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8 and 3National Institute for Nanotechnology (NINT), 11421 Saskatchewan Drive, Edmonton, AB T6G 2M9

*To whom correspondence should be addressed. Tel: +1 780 492 0383; Fax: +1 780 492 1071; Email: david.wishart{at}ualberta.ca

Received February 1, 2007. Revised March 25, 2007. Accepted April 17, 2007.

Protein motions play important roles in numerous biological processes such as enzyme catalysis, muscle contractions, antigen–antibody interactions, gene regulation and virus assembly. Knowledge of protein flexibility is also important in rational drug design, protein docking and protein engineering. However, the experimental measurement of protein motions is often difficult, requiring sophisticated experiments, complex data analysis and detailed information about the protein's tertiary structure. As a result, there is a considerable interest in developing simpler, more effective ways of quantifying protein flexibility. Recently, we described a method, called the random coil index (RCI), which is able to quantitatively estimate backbone root mean square fluctuations (RMSFs) of structural ensembles and order parameters using only chemical shifts. The RCI method is very fast (<5 s) and exceedingly robust. It also offers an excellent alternative to traditional methods of measuring protein flexibility. We have recently extended the RCI concept and implemented it as a web server. This server allows facile, accurate and fully automated predictions of MD RMSF values, NMR RMSF values and model-free order parameters (S2) directly from chemical shift assignments. It also performs automatic chemical shift re-referencing to ensure consistency and reproducibility. On average, the correlation between RCI predictions and experimentally obtained motional amplitudes is within the range from 0.77 to 0.82. The server is available at http://wishart.biology.ualberta.ca/rci.


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