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Preprocessing of rotamers for protein design calculations

✍ Scribed by Premal S. Shah; Geoffrey K. Hom; Stephen L. Mayo

Publisher
John Wiley and Sons
Year
2004
Tongue
English
Weight
101 KB
Volume
25
Category
Article
ISSN
0192-8651

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✦ Synopsis

Abstract

We have developed a process that significantly reduces the number of rotamers in computational protein design calculations. This process, which we call Vegas, results in dramatic computational performance increases when used with algorithms based on the dead‐end elimination (DEE) theorem. Vegas estimates the energy of each rotamer at each position by fixing each rotamer in turn and utilizing various search algorithms to optimize the remaining positions. Algorithms used for this context specific optimization can include Monte Carlo, self‐consistent mean field, and the evaluation of an expression that generates a lower bound energy for the fixed rotamer. Rotamers with energies above a user‐defined cutoff value are eliminated. We found that using Vegas to preprocess rotamers significantly reduced the calculation time of subsequent DEE‐based algorithms while retaining the global minimum energy conformation. For a full boundary design of a 51 amino acid fragment of engrailed homeodomain, the total calculation time was reduced by 12‐fold. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1797–1800, 2004

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