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Bioinformatics Vol. 19 no. 4 2003
Pages 541-542
© 2003 Oxford University Press

Applications Note

3MOTIF: visualizing conserved protein sequence motifs in the protein structure database

Steven P. Bennett 1, Craig G. Nevill-Manning 2,{dagger} and Douglas L. Brutlag 1,*

1 Department of Biochemistry, B400 Beckman Center, Stanford University, CA 94305-5307, USA
2 Computer Science, Rutgers University, Piscataway, NJ 08854, USA

Received on March 6, 2002 ; revised on September 6, 2002 ; accepted on September 10, 2002

Summary: 3MOTIF is a web application that visually maps conserved sequence motifs onto three-dimensional protein structures in the Protein Data Bank (PDB; Berman et al., Nucleic Acids Res., 28, 235–242, 2000). Important properties of motifs such as conservation strength and solvent accessible surface area at each position are visually represented on the structure using a variety of color shading schemes. Users can manipulate the displayed motifs using the freely available Chime plugin.

Availability: http://motif.stanford.edu/3motif/

Contact: brutlag{at}stanford.edu

Supplementary information: http://motif.stanford.edu/3motif/supplementary/

* To whom correspondence should be addressed.

{dagger} Present adress: Google, Inc., 2400 Bayshore Parkway, Mountain View, CA~94043, USA


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