An efficient index-based protein structure database searching method

In this paper, we present a novel indexing method called ProtDex to facilitate fast searching in 3-dimensional protein structure database. In ProtDex, we first build an index on the representative properties of all proteins in the database. When evaluating a query, with the help of the index, we filter out a small candidate list of proteins. Then, we can either directly report them, with their respective rankings, to the user, or do the expensive actual alignments on them upon user´s request. Preliminary experimental results show that our solution is up to 16 times faster than the popular DALI method for database searching task (without actual alignments), while its overall accuracy is only slightly inferior to that of DALI. The software is available upon request by sending emails to the authors.