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PDB2Graph: A toolbox for identifying critical amino acids map in proteins based on graph theory
Niloofar Niknam1, Hamed Khakzad2, Seyed Shahriar Arab1
1Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
Computers in Biology and Medicine
|April 5, 2016
Summary
This study introduces PDB2Graph, a MATLAB toolbox for analyzing protein structure networks. It helps identify critical amino acids, aiding in protein engineering and understanding structural robustness and function.
Area of Science:
- Biophysics
- Structural Biology
- Computational Biology
Background:
- Protein structure analysis benefits from network concepts, integrating topological and global features.
- Network approaches simplify complex biological systems while retaining essential structural and physicochemical properties.
Purpose of the Study:
- To present PDB2Graph, an interactive MATLAB toolbox for constructing, visualizing, and analyzing protein structure networks.
- To identify critical nodes (amino acids) influencing protein structural robustness and function using centrality indices.
Main Methods:
- Development of a user-friendly MATLAB-based toolbox, PDB2Graph.
- Application of network analysis and centrality indices to protein structures.
- Case studies including Calmodulin's structural modification and mutational analysis of model proteins (Phage T4 lysozyme, Barnase, Ribonuclease HI).
Main Results:
- PDB2Graph facilitates the identification of critical amino acids within protein networks.
- The toolbox aids in rationally selecting amino acid candidates for protein structure manipulation.
- Analysis demonstrated the impact of mutations on protein activity, validated by case studies.
Conclusions:
- PDB2Graph is an effective tool for protein structure network analysis, visualization, and identification of key residues.
- The toolbox supports structural biologists in rational protein design and functional studies.
- Network-based analysis provides insights into protein dynamics and the effects of mutations.
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