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. 2009 Jan;37(Database issue):D185-90.
doi: 10.1093/nar/gkn865. Epub 2008 Oct 31.

Minimotif Miner 2nd Release: A Database and Web System for Motif Search

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Free PMC article

Minimotif Miner 2nd Release: A Database and Web System for Motif Search

Sanguthevar Rajasekaran et al. Nucleic Acids Res. .
Free PMC article

Abstract

Minimotif Miner (MnM) consists of a minimotif database and a web-based application that enables prediction of motif-based functions in user-supplied protein queries. We have revised MnM by expanding the database more than 10-fold to approximately 5000 motifs and standardized the motif function definitions. The web-application user interface has been redeveloped with new features including improved navigation, screencast-driven help, support for alias names and expanded SNP analysis. A sample analysis of prion shows how MnM 2 can be used. Weblink: http://mnm.engr.uconn.edu, weblink for version 1 is http://sms.engr.uconn.edu.

Figures

Figure 1.
Figure 1.
Minimotifs predicted by MnM 2 painted onto the surface of prion. (A) Surface plot created from human prion coordinates in PDB accession number 1QM0. The 129V variant that favors Creutzfeldt–Jakob disease eliminates a potential Vav1 SH2 binding motif (yellow) that is present in the 129M variant that favors fatal familial insomnia. Also, the D178N disease-associated mutation eliminates a potential Caspase 1 cleavage site (green/cyan). cCBL TKB domain binding motif (orange), CKII phosphorylation site (red), N-glycosylation motif (magenta) and Grb2 SH2 binding motif (Blue). Several motifs predicted on the opposing face or on missing fragments of the protein are not shown. (B) Output from SNP analysis using MnM 2 website. Minimotifs with red text are eliminated by an SNP and those with green text are introduced by an SNP. SNPs analyzed were M129V and D178V.

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