Automated Protein Design and Sequence Optimisation

Scoring Functions and the Search Problem

A. P. Cootes*, P. M G Curmi, A. E. Torda

*Corresponding author for this work

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)255-271
Number of pages17
JournalCurrent Protein and Peptide Science
Volume1
Issue number3
Publication statusPublished - Nov 2000

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