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ExSer: A standalone tool to mine protein data bank (PDB) for secondary structural elements
Dhandapani Vignesh1, Paul Daniel, Natarajan Raja
1Department of Plant Molecular Biology and Biotechnology, Centre for Plant Molecular Biology, Tamil Nadu Agricultural University, Coimbatore - 641 003, India.
Bioinformation
|October 27, 2010
Summary
This study introduces ExSer, a tool for automatically extracting amino acid sequences for protein secondary structures from Protein Data Bank files. This aids in detailed protein structural analysis.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Detailed protein structural analysis requires examining primary, secondary, and tertiary structures.
- Understanding protein secondary structures (e.g., alpha-helices, beta-strands) is crucial.
- Key information includes encoded amino acid sequences, residue counts, lengths, and composition.
Purpose of the Study:
- To present ExSer, a standalone tool for automated extraction of protein secondary structure information.
- To facilitate the analysis of amino acid sequences within specific secondary structural regions.
Main Methods:
- Development of a standalone software tool named ExSer.
- Automated extraction of secondary structure-encoding amino acid sequences.
- Processing of data from Protein Data Bank (PDB) files.
Main Results:
- ExSer enables automated extraction of amino acid sequences for protein secondary structures.
- The tool processes information directly from PDB files.
- Facilitates detailed analysis of secondary structural elements.
Conclusions:
- ExSer provides an efficient method for obtaining secondary structure sequence data.
- The tool supports in-depth investigation of protein structural organization.
- ExSer is a valuable resource for researchers in structural biology and bioinformatics.
