Searching protein structure databases with DaliLite v.3

UNLABELLED: The Red Queen said, 'It takes all the running you can do, to keep in the same place. ' Lewis Carrol MOTIVATION: Newly solved protein structures are routinely scanned against structures already in the Protein Data Bank (PDB) using Internet servers. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. The number of known structures continues to grow exponentially. Sensitive-thorough but slow-search algorithms are challenged to deliver results in a reasonable time, as there are now more structures in the PDB than seconds in a day. The brute-force solution would be to distribute the individual comparisons on a massively parallel computer. A frugal solution, as implemented in the Dali server, is to reduce the total computational cost by pruning search space using prior knowledge about the distribution of structures in fold space. This note reports paradigm revisions that enable maintaining such a knowledge base up-to-date on a PC. AVAILABILITY: The Dali server for protein structure database searching at http: //ekhidna. biocenter. helsinki. fi/daliₛerver is running DaliLite v. 3. The software can be downloaded for academic use from http: //ekhidna. biocenter. helsinki. fi/daliₗite/downloads/v3.