seeMotif: exploring and visualizing sequence motifs in 3D structures

Abstract

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.

Figure 1.

An example of using seeMotif by combining two motifs from different computational tools. This figure comprises five parts: (1) motifs; (2) position mappings between the motifs and the reference sequence; (3) reference sequence with the matched positions highlighted; (4) a snapshot of the structure panel; and (5) local alignment of the reference sequence and the selected protein chain. In this example, motifs are plotted on the PDB structure 3PRK:E. Protein chains are shown in strands style. The residues matched by any of the motifs are illustrated as sticks with distinct colors corresponding to their sequence expression form in the sequence panel. Ligands (the inhibitor in this structure) are displayed in spacefill and colored in CPK mode.

Figure 2.

An example of using seeMotif by combining five motifs from both computational tools and existing motif databases. This figure comprises five parts: (1) motifs; (2) position mappings between the motifs and the reference sequence; (3) reference sequence with matched positions highlighted; (4) a snapshot of the structure panel; and (5) the motif selection panel in the intermediate page. In this example, motifs are plotted on the PDB structure 1SCJ. Protein chains are shown in strands style, where each chain has its own color. The residues matched by any of the motifs are illustrated as sticks with distinct colors corresponding to their sequence expression form in the sequence panel. CA ions are displayed in spacefill.