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SMotif: a server for structural motifs in proteins.
Ganesan Pugalenthi1, P N Suganthan, R Sowdhamini
1School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798.
Bioinformatics (Oxford, England)
|January 24, 2007
Summary
The SMotif server identifies key protein structural motifs by analyzing sequence and structural features. These identified motifs aid in understanding protein structure, engineering, and folding experiments.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein structure analysis
Background:
- Protein structure analysis is crucial for understanding biological function.
- Identifying conserved structural motifs aids in protein classification and function prediction.
- Existing methods may not fully capture the interplay of sequential and structural features.
Purpose of the Study:
- To introduce the SMotif server for identifying significant protein structural motifs.
- To provide insights into the three-dimensional orientation and spatial arrangement of these motifs.
- To facilitate protein engineering and folding studies by identifying common structural cores.
Main Methods:
- Utilizes conservation of sequential and structural features (solvent accessibility, secondary structure, hydrogen bonding, residue packing).
- Analyzes protein structures to identify conserved structural segments or motifs.
- Determines three-dimensional orientation patterns including inter-motif distances and torsion angles.
Main Results:
- Identifies important structural motifs within protein structures.
- Provides spatial orientation information for identified motifs.
- Highlights potential common cores for protein families.
Conclusions:
- SMotif server effectively identifies conserved protein structural motifs.
- The server's outputs can guide protein engineering and folding experiments.
- Offers a valuable tool for structural biologists and computational chemists.
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Overview