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3dSS: 3D structural superposition.

K Sumathi¹, P Ananthalakshmi, M N A Md Roshan

¹Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India.

Nucleic Acids Research

|July 18, 2006

Summary

The 3dSS server aids researchers in superposing 3D protein structures and identifying common water molecules. It utilizes the RASMOL visualization tool and allows saving atomic coordinates for further analysis.

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Area of Science:

Structural bioinformatics
Computational biology
Molecular modeling

Background:

Superposing multiple 3D protein structures is crucial for comparative analysis.
Identifying conserved water molecules can provide insights into protein-ligand interactions and binding site characteristics.
Existing tools may lack integrated visualization and water molecule analysis capabilities.

Purpose of the Study:

To develop a user-friendly, web-based server for superposing multiple 3D protein structures.
To enable the identification and visualization of invariant or common water molecules within homologous protein structures.
To provide researchers with a tool for saving superposed atomic coordinates for further investigation.

Main Methods:

Development of a web-based interactive computing server named 3dSS.
Integration of the RASMOL molecular visualization tool for client-side visualization.
Utilizing Protein Data Bank (PDB) IDs or uploaded PDB files as input.
Implementation of a system to identify common water molecules in superposed structures.

Main Results:

The 3dSS server successfully superposes multiple 3D protein structures.
The server effectively identifies and visualizes common water molecules in homologous structures.
Users can save the superposed 3D atomic coordinates to their local machine.
The server is accessible via a web interface and uses a regularly updated PDB database.

Conclusions:

3dSS provides a valuable resource for structural bioinformatics research by simplifying the process of structure superposition and water molecule analysis.
The integrated visualization and data saving features enhance the utility of the server for researchers.
The web-based accessibility makes 3dSS a convenient tool for the scientific community.

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