Clustering techniques for protein surfaces

Though most approaches to protein comparison are based on their structure, several studies produced evidence of a strict correlation between the surface characteristics of proteins and the way they interact. Surface-based techniques for protein comparison typically require applying clustering algorithms to the punctual 3D description of the surface in order to produce a compact surface representation, capable of effectively condensing its description. In this paper, we propose a formalization of the requirements for surface clustering in the biochemical context and present two different clustering techniques that meet them, based, respectively, on region-growing and on an original template matching algorithm. We discuss the validity of these techniques with the support of tests performed on a set of about one hundred protein models generated by punctual mutations of four structurally characterized proteins. Finally, an analysis is made of how different factors impact on the effectiven...

• Type: Journal
• Year: 2006
• Where: PR
• Authors: Lorenzo Baldacci, Matteo Golfarelli, Alessandra Lumini, Stefano Rizzi
• Keywords: Compact Surface Representation, PR 2006, Proteins, Punctual 3D Description