Nucleic Acids Research Advance Access published online on May 28, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp439
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seeMotif: exploring and visualizing sequence motifs in 3D structures
1Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, 2Department of Computer Science and Information Engineering and 3Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei, 10617, Taiwan, R.O.C.
*To whom correspondence should be addressed. Tel: +886 2 3366 5334; Fax: +886 2 2362 7620; Email: cychen{at}mars.csie.ntu.edu.tw
Received March 4, 2009. Revised April 23, 2009. Accepted May 11, 2009.
Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally, characterizing the functional roles of motifs and identifying the potential synergetic relationships between them are important next steps. A good way to investigate novel motifs is to utilize the abundant 3D structures that have also been accumulated at an astounding rate in recent years. This article reports the development of the web service seeMotif, which provides users with an interactive interface for visualizing sequence motifs on protein structures from the Protein Data Bank (PDB). Researchers can quickly see the locations and conformation of multiple motifs among a number of related structures simultaneously. Considering the fact that PDB sequences are usually shorter than those in sequence databases and/or may have missing residues, seeMotif has two complementary approaches for selecting structures and mapping motifs to protein chains in structures. As more and more structures belonging to previously uncharacterized protein families become available, combining sequence and structure information gives good opportunities to facilitate understanding of protein functions in large-scale genome projects. Available at: http://seemotif.csie.ntu.edu.tw,http://seemotif.ee.ncku.edu.tw or http://seemotif.csbb.ntu.edu.tw.