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Current Protein & Peptide Science


ISSN (Print): 1389-2037
ISSN (Online): 1875-5550

Automated Protein Design and Sequence Optimisation Scoring Functions and the Search Problem

Author(s): A. P. Cootes, P. M.G. Curmi and A. E. Torda

Volume 1, Issue 3, 2000

Page: [255 - 271] Pages: 17

DOI: 10.2174/1389203003381351

Price: $65


Advances in molecular biology may mean that almost any protein sequence can be synthesised, but perhaps this has served to highlight the inadequacy of theoretical work. For a given protein fold, it is probably not possible to reliably predict an ideal sequence. We identify and survey several aspects of the problem. Firstly, it is not clear what is the best way to score a sequence-structure pair. Secondly, there is no consensus as to what the score function should represent (free energy or some abstract measure of sequence-structure compatibility). Finally, the number of possible sequences is astronomical and searching this space poses a daunting optimisation problem. These problems are discussed in the light of recent experimental successes.

Keywords: Automated Protein Design, Mutagenesis, Protein data bank PDB, Statistical Analysis, Negative design

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