Can We Determine a Protein Structure Quickly?
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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''.
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