Journal of Computer Science and Technology  2010, 25(1) 95-106 DOI:     ISSN: 1000-9000 CN: CN 11-2296/TP
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Keywords
automated NMR (Nuclear Magnetic Resonance)
protein structure determination
algorithms
Authors
Ming Li

Can We Determine a Protein Structure Quickly?

Ming Li (李明), Fellow, ACM, IEEE, Royal Society of Canada

D.R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, N2L 3G1 Canada
Dingsheng Technologies, Beijing 100085, China

Abstract：

Can we determine a high resolution protein structure quickly, say, in a week? I will show this is possible by the current technologies together with new computational tools discussed in this article. We have three potential paths to explore:

 

 

 

 

  • X-ray crystallography. While this method has produced the most protein structures in the PDB (Protein Data Bank), the nasty trial-and-error crystallization step remains to be an inhibitive obstacle.
  • NMR (Nuclear Magnetic Resonance) spectroscopy. While the NMR experiments are relatively easy to do, the interpretation of the NMR data for structure calculation takes several months on average.
  • In silico protein structure prediction. Can we actually predict high resolution structures consistently? If the predicted models remain to be labeled as ``predicted'', and these structures still need to be experimentally verified by the wet lab methods, then this method at best can serve only as a screening tool.
    I investigate the question of ``quick protein structure determination'' from a computer scientist point of view and actually answer the more relevant question ``what can a computer scientist effectively contribute to this goal''.

     

     

     

     

     

    • Keywords： automated NMR (Nuclear Magnetic Resonance)    protein structure determination    algorithms  
    Received: 2009-10-13 Accepted: 2009-11-16 Online:  
    DOI:
    Fund:

    This work was partially supported by the National High Tech Research and Development 863 Program under Grant No. 2008AA02Z313 from China's Ministry of Science and Technology, Canada's NSERC under Grant No. OGP0046506, Canada Research Chair Program, an NSERC Collaborative Grant, and Ontario's Premier's Discovery Award.

    Email: mli@uwaterloo.ca
    About author(s):
    Ming Li is a Canada research chair in bioinformatics and a University Professor at the University of Waterloo. He is a fellow of Royal Society of Canada, ACM, and IEEE. He is a recipient of E.W.R. Steacie Fellowship Award in 1996, and the 2001 Killam Fellowship. Together with Paul Vitanyi he has pioneered the applications of Kolmogorov complexity and co-authored the book ``An introduction to Kolmogorov complexity and its applications''. His research interests recently include protein structure determination and the Internet search engine.
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