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Computational Alanine Scanning with Linear Scaling Semiempirical Quantum Mechanical Methods by David J. Diller; Christine Humblet; Xiaohua Zhang; Lance M. Westerhoff is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is Computational Alanine Scanning with Linear Scaling Semiempirical Quantum Mechanical Methods about?

## Abstract Alanine scanning is a powerful experimental tool for understanding the key interactions in protein–protein interfaces. Linear scaling semiempirical quantum mechanical calculations are now sufficiently fast and robust to allow meaningful calculations on large systems such as proteins, RNA and DNA. In particular, they have proven useful in understanding protein–ligand interactions. Here we ask the question: can these linear scaling quantum mechanical methods developed for protein–ligand scoring be useful for computational alanine scanning? To answer this question, we assembled 15 protein–protein complexes with available crystal structures and sufficient alanine scanning data. In all, the data set contains ΔΔ__G__s for 400 single point alanine mutations of these 15 complexes. We show that with only one adjusted parameter the quantum mechanics‐based methods outperform both buried accessible surface area and a potential of mean force and compare favorably to a variety of published empirical methods. Finally, we closely examined the outliers in the data set and discuss some of the challenges that arise from this examination. Proteins 2010. © 2010 Wiley‐Liss, Inc.

Who reads Computational Alanine Scanning with Linear Scaling Semiempirical Quantum Mechanical Methods?

Author

David J. Diller; Christine Humblet; Xiaohua Zhang; Lance M. Westerhoff

Publisher

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

Published

2010

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)