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. 2004 Jul 1;32(Web Server issue):W536-41.
doi: 10.1093/nar/gkh389.

FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web

Jessica Shapiro  1 , Douglas Brutlag
Affiliations

FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web

Jessica Shapiro et al. Nucleic Acids Res. .

Abstract

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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Figures

Figure 1
Figure 1
The motif window. The motif window displays the core of SCOP's immunoglobulin-like fold as represented in 1neu, the query structure for this search. The right-hand portion of the window shows both the motif definition in the form of conservation values and options for manual refinement as described in the text. Black arrows indicate the three SSEs that are insertions with respect to the core fold, and blue arrows indicate the two strands detected by DSSP that both correspond to the first strand of the core fold.
Figure 2
Figure 2
The FoldMiner server alignment viewer. The alignment of the query, 1neu, to a cupredoxin target (SCOP domain d1ycsa_) is colored by SSE alignment scores. The alignment viewer provides a number of customized options for viewing and analyzing superpositions and an interface that allows for the execution of arbitrary sequences of Chime commands.
See this image and copyright information in PMC

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