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Published on: April 26, 2013
A Web-based classification system of DNA-binding protein families
M Karmirantzou1, S J Hamodrakas
1Faculty of Biology, Department of Cell Biology and Biophysics, University of Athens, Panepistimiopolis, Athens 157 01, Greece.
Protein Engineering
|August 28, 2001
Summary
This study presents DnaProt, a web-based resource for classifying DNA-binding proteins. It organizes 3238 protein sequences into 33 classes using functional motifs, aiding genome analysis.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Rational classification of proteins from sequenced genomes is crucial for functional and evolutionary studies.
- DNA-binding proteins are a highly populated and studied protein family across bacteria, archaea, and eukaryotes.
Purpose of the Study:
- To develop a web-based system for the rational classification of DNA-binding proteins.
- To create an annotated and searchable collection of DNA-binding protein sequences.
Main Methods:
- Collected 3238 full-length DNA-binding protein sequences from SWISS-PROT release 38.
- Organized sequences into families using PROSITE patterns, PRINTS motifs, and de novo excised signatures.
- Combined global similarities and functional motifs to classify proteins into 33 unique classes.
Main Results:
- The DnaProt resource provides a classification scheme for DNA-binding proteins based on sequence similarity and functional motifs.
- Identified 33 distinct classes of DNA-binding proteins, revealing comprehensive family relationships.
- Included multiple alignments for each family and referenced structural class representatives.
Conclusions:
- DnaProt facilitates efficient retrieval and analysis of DNA-binding protein data through its web-based system.
- The classification scheme aids in understanding protein function and evolutionary relationships.
- The resource offers free online access to customized datasets and hyperlinked entries for easy data retrieval.
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