From structure to sequence and back again

Journal of Molecular Biology
D A Hinds, M Levitt

Abstract

With a simple lattice model and sequence design algorithm, we can design sequences to fit arbitrary compact globular structures. We judged the success of the design algorithm by performing exhaustive conformational searches to determine if a designed sequence's lowest energy conformation matched the target for which it was designed. Designed sequences tend to be much better optimized for their targets than a natural sequence is optimized for its lowest energy model conformation. We examined the effect of varying the number of available amino acid types on the success of the design method. It was more difficult but not impossible to successfully design discriminating sequences using fewer amino acid types.

Citations

Jan 1, 1997·Annual Review of Physical Chemistry·J N OnuchicP G Wolynes
Jul 15, 2006·PLoS Computational Biology·Feng Ding, Nikolay V Dokholyan
Oct 29, 2005·The Journal of Chemical Physics·Parbati BiswasJeffery G Saven
Sep 2, 1998·Proceedings of the National Academy of Sciences of the United States of America·E D Nelson, J N Onuchic
Feb 1, 1997·Protein Science : a Publication of the Protein Society·D K Agrafiotis
Nov 17, 2001·Chemical Reviews·J G Saven

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