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Protein family clustering for structural genomics
1Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
Journal of Molecular Biology
|September 28, 2005
Summary
Structural genomics aims to provide protein domain templates. This study estimates 250,000 protein families from 1000 microbial genomes, with 70-80% coverage achievable by sampling large families.
Area of Science:
- Genomics
- Structural Biology
- Bioinformatics
Background:
- Structural genomics endeavors to create structural templates for a significant portion of protein domains.
- Estimating the number and diversity of protein sequence families is crucial for this goal.
- Fully sequenced bacterial genomes offer opportunities for improved family estimations.
Purpose of the Study:
- To assess current structure coverage for known protein families.
- To predict the growth of protein families with increasing genome sequencing.
- To devise a strategy for maximizing structural template coverage.
Main Methods:
- Utilized an automated clustering procedure to group protein sequences from multiple genomes into families.
- Bench-marked the clustering method for sensitivity in detecting remote family members and minimizing false positives.
- Analyzed the resulting comprehensive protein family set against existing structural data.
Main Results:
- Approximately 20% of known protein families (with >= 3 members) currently possess a representative structure.
- An estimated 250,000 protein families will exist after sequencing 1000 microbial genomes.
- The majority of these families are small; structural templates for 70-80% of protein domains are attainable.
Conclusions:
- Current structure coverage for protein families is limited.
- The number of protein families is larger than previously anticipated.
- A focused strategy on sampling larger families can efficiently maximize structural coverage.