Motivation. Computational methods to predict protein-protein interactions are of great need. They can help to formulate hypotheses, guide experimental research and serve as additional measures to assess the quality of data obtained in high-throughput interaction experiments. Here, we describe a fully automated threestep ...

The main contribution of this paper is a novel approach for fast searching in huge structural databases like the PDB. The data structure is based on an adaption of the generalized suffix tree and relies on an translationand rotation-invariant representation of the protein backbone. The method was evaluated by applying ...