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Bioinformatics Advance Access originally published online on November 21, 2006
Bioinformatics 2007 23(3):378-380; doi:10.1093/bioinformatics/btl585
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© 2006 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.

NvMap: automated analysis of NMR chemical shift perturbation data

Lisa Fukui and Yuan Chen *

Division of Immunology, Beckman Research Institute of the City of Hope 1450 East Duarte Road, Duarte, CA 91010, USA

*To whom correspondence should be addressed.


  Abstract

Summary: NMR chemical shift perturbation experiments are widely used to define binding sites in biomolecular complexes. Especially in the case of high throughput screening of ligands, rapid analysis of NMR spectra is essential. NvMap extends NMRViewJ and provides a means for rapid assignments and book-keeping of NMR titration spectra. Our module offers options to analyze multiple titration spectra both separately and sequentially, where the sequential spectra are analyzed either two at a time or all simultaneously. The first option is suitable for slow or intermediate exchange rates between free and bound proteins. The latter option is particularly useful for fast exchange situations and can compensate for the lack of indicators for overlapped peaks. Our module also provides a simple user interface to automate the analysis process from dataset to peak list. We demonstrate the effectiveness of our program using NMR spectra of SUMO in complexes with three different peptides.

Availability: NvMap is available on the web at http://www.cityofhope.org/Researchers/ChenYuan/NvMap/

Contact: ychen{at}coh.org

Supplemental information: Manual pages and test spectra will be available on the web at the above site.

Associate Editor: Keith A Crandall

Received on June 7, 2006; revised on November 15, 2006; accepted on November 16, 2006

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