On using energy signatures in protein structure similarity searching

Abstract

The analysis of small molecular substructures (like enzyme active sites) in the whole protein structure can be supported by using methods of similarity searching. These methods allow to search the 3D structural patterns in a database of protein structures. However, the well-known methods of fold similarity searching like VAST or DALI are not appropriate for this task. Methods that benefit from a dependency between a spatial conformation and potential energy of protein structure seem to be more supportive. In the paper, we present a new version of the EAST (Energy Alignment Search Tool) algorithm that uses energy signatures in the process of similarity searching. This makes the algorithm not only more sensitive, but also eliminates disadvantages of previous implementations of our EAST method. © 2008 Springer-Verlag Berlin Heidelberg.