FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web
1 Biophysics Program and 2 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
* To whom correspondence should be addressed. Tel: +1 650 723 6593; Fax: +1 650 723 6783; Email: brutlag{at}stanford.edu
Received February 13, 2004; Revised and Accepted March 24, 2004
The FoldMiner web server (http://foldminer.stanford.edu/) provides remote access to methods for protein structure alignment and unsupervised motif discovery. FoldMiner is unique among such algorithms in that it improves both the motif definition and the sensitivity of a structural similarity search by combining the search and motif discovery methods and using information from each process to enhance the other. In a typical run, a query structure is aligned to all structures in one of several databases of single domain targets in order to identify its structural neighbors and to discover a motif that is the basis for the similarity among the query and statistically significant targets. This process is fully automated, but options for manual refinement of the results are available as well. The server uses the Chime plugin and customized controls to allow for visualization of the motif and of structural superpositions. In addition, we provide an interface to the LOCK 2 algorithm for rapid alignments of a query structure to smaller numbers of user-specified targets.
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