Fast Structure Searching for Computational Proteomics
Hanjo Täubig · mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) · 2007
Proteins are among the most important organic compounds. The vast number of their functions are based on the specific effect of their various structures. To investigate the principles of protein structure and function experimentally determined structures were collected in the Protein Data Bank since 1971. Searching in this database is essential for protein research. At the moment, the only way to perform a search in an acceptable amount of time is by sequence or as a full-text search. In this work, we propose a search method that is based on the three-dimensional structure of proteins. From discretized torsion angles we create translation- and rotation-invariant representations which are stored in a generalized suffix tree. Queries are then performed as tolerant searches in this tree. Experiments demonstrate faster query response times while maintaining similar accuracy of search results when compared with conventional methods.