TY - JOUR
T1 - Automated Protein Design and Sequence Optimisation
T2 - Scoring Functions and the Search Problem
AU - Cootes, A. P.
AU - Curmi, P. M.G.
AU - Torda, A. E.
PY - 2000/11
Y1 - 2000/11
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=0034334330&partnerID=8YFLogxK
U2 - 10.2174/1389203003381351
DO - 10.2174/1389203003381351
M3 - Article
SN - 1389-2037
VL - 1
SP - 255
EP - 271
JO - Current Protein and Peptide Science
JF - Current Protein and Peptide Science
IS - 3
ER -