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Ramachandran plot on the web (2.0).

K Gopalakrishnan¹, G Sowmiya, S S Sheik

¹Bioinformatics Centre (Centre of Excellence in Structural Biol. & Bio-comput.), Indian Institute of Science, Bangalore 560 012, India.

Protein and Peptide Letters

|September 28, 2007

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This study presents an updated Ramachandran plot web server for visualizing protein main chain conformation angles (Phi and Psi). The enhanced server offers improved display options for various regions and secondary structures.

Area of Science:

Biochemistry and Structural Biology
Computational Biology and Bioinformatics

Background:

The Ramachandran plot is a fundamental tool for analyzing protein structure, illustrating the allowed and disallowed combinations of main chain dihedral angles (Phi and Psi).
Understanding protein conformation is crucial for drug discovery and protein engineering.

Purpose of the Study:

To report an updated version of the Ramachandran plot web server with enhanced visualization capabilities.
To provide users with improved options for analyzing protein main chain conformation angles.

Main Methods:

Development and implementation of an updated web server for Ramachandran plot generation.
Inclusion of advanced display options for conformation angles in specific regions and secondary structural elements.
Integration of user-defined Phi and Psi value filtering for customized analysis.

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Main Results:

The updated web server offers improved visualization of protein main chain conformation angles (Phi and Psi).
New features allow detailed analysis of angles within specific secondary structures and user-defined plot regions.
The server provides enhanced options for exploring protein conformational space.

Conclusions:

The updated Ramachandran plot web server is a valuable resource for protein structure analysis.
Enhanced visualization and customization options facilitate a deeper understanding of protein folding and stability.
The tool supports researchers in structural biology and bioinformatics.