Related Experiment Videos
3MOTIF: visualizing conserved protein sequence motifs in the protein structure database
Steven P Bennett1, Craig G Nevill-Manning, Douglas L Brutlag
1Department of Biochemistry, B400 Beckman Center, Stanford University, CA 94305-5307, USA.
Bioinformatics (Oxford, England)
|March 4, 2003
Summary
3MOTIF is a web tool that maps conserved sequence motifs onto protein structures. It visually represents motif properties like conservation strength and accessibility on 3D protein models.
Area of Science:
- Bioinformatics
- Structural Biology
- Computational Biology
Background:
- The Protein Data Bank (PDB) is a crucial resource for structural biology.
- Identifying and visualizing conserved sequence motifs is essential for understanding protein function and evolution.
Purpose of the Study:
- To develop a web application for visualizing conserved sequence motifs on protein 3D structures.
- To provide insights into motif properties such as conservation strength and solvent accessibility.
Main Methods:
- Developed the 3MOTIF web application.
- Integrated visualization of conserved sequence motifs onto Protein Data Bank (PDB) structures.
- Utilized color shading schemes to represent motif properties like conservation strength and solvent accessible surface area.
Main Results:
- 3MOTIF successfully maps conserved sequence motifs onto protein structures.
- Visual representations highlight key motif properties on the 3D protein models.
- Users can interactively manipulate motif displays using the Chime plugin.
Conclusions:
- 3MOTIF offers a valuable tool for researchers studying protein sequence motifs and structures.
- The application enhances the understanding of motif conservation and its relationship to protein structure and function.
- Web-based visualization facilitates the exploration of complex biological data.