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Automated Scaffold Selection for Enzyme Design by Christoph Malisi; Oliver Kohlbacher; Birte Höcker is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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## Abstract A major goal of computational protein design is the construction of novel functions on existing protein scaffolds. There the first question is which scaffold is suitable for a specific reaction. Given a set of catalytic residues and their spatial arrangement, one wants to identify a protein scaffold that can host this active site. Here, we present an algorithm called ScaffoldSelection that is able to rapidly search large sets of protein structures for potential attachment sites of an enzymatic motif. The method consists of two steps; it first identifies pairs of backbone positions in pocket‐like regions. Then, it combines these to complete attachment sites using a graph theoretical approach. Identified matches are assessed for their ability to accommodate the substrate or transition state. A representative set of structures from the Protein Data Bank (∼3500) was searched for backbone geometries that support the catalytic residues for 12 chemical reactions. Recapitulation of native active site geometries is used as a benchmark for the performance of the program. The native motif is identified in all 12 test cases, ranking it in the top percentile in 5 out of 12. The algo

Who reads Automated Scaffold Selection for Enzyme Design?

Author

Christoph Malisi; Oliver Kohlbacher; Birte Höcker

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)

Published

2009

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)