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SEM (Symmetry Equivalent Molecules): A web-based GUI to generate and visualize the macromolecules
A S Z Hussain1, Ch Kiran Kumar, C K Rajesh
1Bioinformatics Centre, Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, 560 012, India.
Nucleic Acids Research
|June 26, 2003
Summary
Symmetry Equivalent Molecules (SEM) is a web tool that generates and visualizes symmetry-related protein and nucleic acid structures. Users can save 3D atomic coordinates for further analysis.
Area of Science:
- Structural Biology
- Computational Biology
- Bioinformatics
Background:
- Understanding molecular symmetry is crucial in structural biology.
- Visualizing symmetry-equivalent molecules aids in analyzing protein and nucleic acid structures.
Purpose of the Study:
- To develop a user-friendly web-based tool for generating and visualizing symmetry-equivalent molecules.
- To provide researchers with the ability to save 3D atomic coordinates of these molecules.
Main Methods:
- Developed a web-based graphical user interface (GUI) using CGI/Perl scripts.
- Integrated the program with the Protein Data Bank (PDB) containing X-ray crystallography structures.
- Utilized the RasMol program for visualization of molecular structures.
Main Results:
- Successfully created Symmetry Equivalent Molecules (SEM), a tool for generating and visualizing symmetry-related molecular structures.
- Enabled users to save the 3D atomic coordinates of symmetry-equivalent molecules.
- Interfaced SEM with all 3D structures in the PDB.
Conclusions:
- SEM provides a valuable resource for structural biologists and computational chemists.
- The tool facilitates the study of symmetry in proteins and nucleic acids.
- SEM is accessible via a web interface for widespread use.