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Smartnotebook: A semi-automated approach to protein sequential NMR resonance assignments

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Abstract

Complete and accurate NMR spectral assignment is a prerequisite for high-throughput automated structure determination of biological macromolecules. However, completely automated assignment procedures generally encounter difficulties for all but the most ideal data sets. Sources of these problems include difficulty in resolving correlations in crowded spectral regions, as well as complications arising from dynamics, such as weak or missing peaks, or atoms exhibiting more than one peak due to exchange phenomena. Smartnotebook is a semi-automated assignment software package designed to combine the best features of the automated and manual approaches. The software finds and displays potential connections between residues, while the spectroscopist makes decisions on which connection is correct, allowing rapid and robust assignment. In addition, smartnotebook helps the user fit chains of connected residues to the primary sequence of the protein by comparing the experimentally determined chemical shifts with expected shifts derived from a chemical shift database, while providing bookkeeping throughout the assignment procedure.

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Authors and Affiliations

  1. Protein Engineering Network Centers of Excellence, 713 Heritage Medical Research Center, University of Alberta, Edmonton, Alberta, T6G 2S2, Canada

    Carolyn M. Slupsky, Robert F. Boyko, Valerie K. Booth & Brian D. Sykes

Authors
  1. Carolyn M. Slupsky
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  2. Robert F. Boyko
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  3. Valerie K. Booth
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  4. Brian D. Sykes
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Correspondence to Brian D. Sykes.

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Slupsky, C.M., Boyko, R.F., Booth, V.K. et al. Smartnotebook: A semi-automated approach to protein sequential NMR resonance assignments. J Biomol NMR 27, 313–321 (2003). https://doi.org/10.1023/A:1025870122182

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