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DBAC: A simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts by Zhenhua Li; Limsoon Wong; Jinyan Li is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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## Background A protein binding hot spot is a cluster of residues in the interface that are energetically important for the binding of the protein with its interaction partner. Identifying protein binding hot spots can give useful information to protein engineering and drug design, and can also deepen our understanding of protein-protein interaction. These residues are usually buried inside the interface with very low solvent accessible surface area (SASA). Thus SASA is widely used as an outstanding feature in hot spot prediction by many computational methods. However, SASA is not capable of distinguishing slightly buried residues, of which most are non hot spots, and deeply buried ones that are usually inside a hot spot. ## Results We propose a new descriptor called “burial level” for characterizing residues, atoms and atomic contacts. Specifically, burial level captures the depth the residues are buried. We identify different kinds of deeply buried atomic contacts (DBAC) at different burial levels that are directly broken in alanine substitution. We use their numbers as input for SVM to classify between hot spot or non hot spot residues. We achieve F measure of 0.6237 under the l

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Author

Zhenhua Li; Limsoon Wong; Jinyan Li

Publisher

BioMed Central; Springer (Biomed Central Ltd.); London: BioMed Central, [2006]-; Springer Science and Business Media LLC (ISSN 1752-0509)

Published

2011

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)