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NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions
N M Luscombe1, R A Laskowski, J M Thornton
1Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, UK.
Nucleic Acids Research
|February 28, 1998
Summary
NUCPLOT is a new program that automatically analyzes protein-DNA interactions from 3D structures. It generates clear plots of binding residues, aiding in the understanding of genetic activity and facilitating comparisons between different protein-DNA complexes.
Area of Science:
- Structural Biology
- Bioinformatics
- Molecular Biology
Background:
- Proteins interacting with DNA are crucial for genetic activity.
- Understanding protein-DNA binding sites and interactions is key to deciphering their functions.
- Analysis of these interactions aids in comprehending nucleic acid interactions.
Purpose of the Study:
- To introduce NUCPLOT, a novel program for automated analysis of protein-DNA interactions.
- To generate schematic visualizations of protein-DNA binding interfaces from 3D atomic coordinates.
- To facilitate the study and comparison of binding modes across various protein-nucleic acid complexes.
Main Methods:
- Utilizes 3D atomic coordinates from Protein Data Bank (PDB) files.
- Employs an automated computational approach to identify binding residues and interactions.
- Generates schematic plots illustrating hydrogen, van der Waals, and covalent bonds.
Main Results:
- NUCPLOT successfully identifies and visualizes protein-DNA interactions.
- The program produces clear and simple PostScript output files of binding interfaces.
- Identified interactions include hydrogen bonds, van der Waals forces, and covalent bonds.
Conclusions:
- NUCPLOT provides an automated and efficient method for analyzing protein-DNA binding.
- The generated plots offer immediate insights into critical interactions within protein-nucleic acid complexes.
- The program is applicable to diverse protein-DNA complexes and some protein-RNA structures.