W58 Nucleic Acids Research, 2010, Vol. 38, Web Server issue family, they are denoted as good results. As the global comparison method introduces new features to improve the system performance, on average, our system’s global search exhibits 97.04% precision at the 10% recall rate and 87.82% precision at the 100% recall rate. A query using the protein chain with the maximum length in the testing set, 566 Ca atoms, takes 3.37 s to return the ranked search results. These tests were conducted on a Linux distributed system consisting of ﬁve servers (13). We applied the local comparison method to SCOP fold classiﬁcation and compared its performance with known algorithms, such as DALI (2), CE (3), MultiProt (18), SSM (19) and MAMMOTH (20), on a non-redundant database of 3276 protein chains selected from PDBSelect and SCOP v1.73. Our system was able to return ranked results in 182 s for query protein structures with an average length of 167 residues, which is 53.10, 10.87, 3.60 and 1.64 times faster than DALI, CE, MultiProt and MAMMOTH, respectively. Evaluated on three diﬀer- ent data sets of non-redundant proteins from SCOP, the average accuracy of our system is approximately equal to DALI, better than MAMMOTH and signiﬁcantly better than CE, MultiProt and SSM. These tests were conducted on a Linux Fedora server with AMD Opteron dual-core 1000 series processors and 2GB RAM (14). DISCUSSION Over the past decade, we have witnessed a rapidly increasing number of protein structures, which poses a great challenge to search engines that retrieve structurally similar proteins. The ProteinDBS v2.0 web server pre- sented in this article comes equipped with an eﬃcient and accurate search engine, a large-scale protein structure database and a more user-friendly interface. ProteinDBS can return accurate results in seconds for global structure search and takes much less time for local structural searches compared to other accurate comparison methods while preserving higher or similar accuracy. It is expected that this web server will be beneﬁcial to the life sciences community for comparative structural analysis, automatic fold classiﬁcation and the discovery of functional and evolutionary connections between protein structures. ACKNOWLEDGEMENTS The authors are grateful to the researchers and groups who made the following software packages and databases available for us to use in ProteinDBS: the Jmol package (http://jmol.sourceforge.net/), which generates view of aligned proteins, the SCOP database for ground truth testing (15), and the PDB (http://www.pdb.org) for main- taining the tertiary structures. FUNDING Shumaker Endowment in Bioinformatics. Funding for open access charge: University of Missouri Shumaker Endowment in Bioinformatics. 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