Minimotif Miner: A Computational Tool to Investigate Protein Function, Disease, and Genetic Diversity

Martin R. Schiller1

1 University of Connecticut Health Center, Farmington, Connecticut
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 2.12
DOI:  10.1002/0471140864.ps0212s48
Online Posting Date:  May, 2007
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Abstract

The Minimotif Miner Web site contains information on several hundred short functional motifs in a single database, and allows the user to search protein queries for the presence of these motifs. Scoring based on evolutionary conservation, protein surface prediction, and motif frequency can be used in conjunction with other motif programs and the known biology of the query to reduce falseā€positive predictions and select short motifs for experimental pursuit.

Keywords: motif; minimotif; proteome; evolution; disease

     
 
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Table of Contents

  • Mapping and Ranking Motifs with Minimotif Miner
  • Interpretation and Selecting Motifs
  • Mapping Motifs onto Protein Surfaces
  • Using Minimotif Miner to Investigate Disease and Genetic Diversity
  • Discussion
  • Acknowledgements
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

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Figures

Videos

Literature Cited

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Key References
   Balla et al., 2006. See above.
  Describes the MnM database, algorithms used in scoring, and methods used to validation the scoring approaches.
Internet Resources
   http://mnm.engr.uconn.edu
  Minimotif Miner (MnM):,Online Web site for identifying short functional motifs.
   http://pymol.sourceforge.net/
  PyMOL: Shareware software for viewing motifs in protein structures.
   http://hugin.ethz.ch/wuthrich/software/molmol/index.html
  MolMol: Downloadable software for viewing protein structures.
   http://www.rcsb.org/pdb/
  Protein Data Bank (PDB): Repository of macromolecular structures.
   http://www.ncbi.nlm.nih.gov/omim/
  McKusick, V.A. 2000. Online Mendelian Inheritance in Man (OMIM). McKusick‐Nathans Institute for Genetic Medicine, Johns Hopkins University, (Baltimore, Md. and National Center for Biotechnology Information, National Library of Medicine, Bethesda, Md.
   http://elm.eu.org/
  ELM: Online Web site for identifying short functional motifs.
   http://myhits.isb‐sib.ch/cgi‐bin/pattern_search
  myHITS (pattern search): Searches several sequence databases for motifs.
   http://www.ncbi.nlm.nih.gov/BLAST/
  BLAST: Searches proteins for short, nearly exact matches.
   http://scansite.mit.edu/motifscan_seq.phtml
  SCANSITE: Online Web site for identifying short functional motifs.
   http://ca.expasy.org/tools/
  ExPASy: Contains a collection of tools for prediction of specific motifs.
   http://www.hgmd.cf.ac.uk/ac/index.php
  HGMD: The Human Genome Mutations Database, which contains a large collection of mutations known to be associated with human disease.
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