P3S: Protein structure similarity search

Abstract

Similarity search in protein structure databases is an important task of computational biology. To reduce the time required to search for similar structures, indexing techniques are being often introduced. However, as the indexing phase is computationally very expensive, it becomes useful only when a large number of searches are expected (so that the expensive indexing cost is amortized by cheaper search cost). This is a typical situation for a public similarity search service. In this article we introduce the P3S web application (http://siret.cz/p3s) allowing, given a query structure, to identify the set of the most similar structures in a database. The result set can be browsed interactively, including visual inspection of the structure superposition, or it can be downloaded as a zip archive. P3S employs the SProt similarity measure and an indexing technique based on the LAESA method, both introduced recently by our group. Together with the measure and the index, the method presents an effective and efficient tool for querying protein structure databases. © 2013 Springer-Verlag.