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New tools and resources for analysing protein structures and their interactions.
N M Luscombe1, R A Laskowski, D R Westhead
1Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, England.
Summary
New software tools simplify the analysis of protein structures. These resources, including PDBsum and TOPS, aid researchers in studying protein topology and interactions.
Area of Science:
- Structural biology
- Bioinformatics
- Computational chemistry
Background:
- Protein structure determination is crucial for understanding protein function.
- The Protein Data Bank (PDB) contains a vast number of protein structures.
- Efficient tools are needed to analyze these large datasets.
Purpose of the Study:
- To present new software tools for detailed protein structure analysis.
- To facilitate the study of protein topology, DNA-binding, and protein-protein interactions.
- To provide accessible web-based resources for structural bioinformatics.
Main Methods:
- Development of the PDBsum website for summarizing PDB entries.
- Implementation of TOPS and NUCPLOT programs for schematic diagram generation.
- Creation of SAS, a web-based sequence analysis tool with structural data integration.
- Establishment of WWW servers for analyzing protein interfaces and haem-binding proteins.
Main Results:
- PDBsum offers comprehensive summaries of all PDB entries.
- TOPS and NUCPLOT visualize protein topology and DNA interactions.
- SAS integrates structural data into sequence analysis.
- Specialized servers enable detailed analysis of protein interfaces and haem-binding proteins.
Conclusions:
- The presented software tools enhance the accessibility and depth of protein structure analysis.
- These resources streamline the investigation of protein structure-function relationships.
- The developed tools support researchers in structural biology and bioinformatics.