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Identifying and Reducing Error in Cluster-expansion Approximations of Protein Energies by Seungsoo Hahn; Orr Ashenberg; Gevorg Grigoryan; Amy E. Keating is a Chemistry article available to read on EtoBox.

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## Abstract Protein design involves searching a vast space for sequences that are compatible with a defined structure. This can pose significant computational challenges. Cluster expansion is a technique that can accelerate the evaluation of protein energies by generating a simple functional relationship between sequence and energy. The method consists of several steps. First, for a given protein structure, a training set of sequences with known energies is generated. Next, this training set is used to expand energy as a function of clusters consisting of single residues, residue pairs, and higher order terms, if required. The accuracy of the sequence‐based expansion is monitored and improved using cross‐validation testing and iterative inclusion of additional clusters. As a trade‐off for evaluation speed, the cluster‐expansion approximation causes prediction errors, which can be reduced by including more training sequences, including higher order terms in the expansion, and/or reducing the sequence space described by thecluster expansion. This article analyzes the sources of error and introduces a method whereby accuracy can be improved by judiciously reducing the described sequen

Who reads Identifying and Reducing Error in Cluster-expansion Approximations of Protein Energies?

Author

Seungsoo Hahn; Orr Ashenberg; Gevorg Grigoryan; Amy E. Keating

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); John Wiley & Sons Inc.; Wiley (ISSN 0192-8651)

Published

2010

Language

EN

Field

Chemistry (Physical Sciences)