Related Experiment Videos
The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms
Liam J McGuffin1, Stefano A Street, Kevin Bryson
1Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK.
Nucleic Acids Research
|December 19, 2003
Summary
The Genomic Threading Database (GTD) provides structural assignments for proteins from eukaryotes and prokaryotes. This method accurately predicts protein folds and residue alignments, aiding genomic research.
Area of Science:
- Bioinformatics
- Structural Biology
- Genomics
Background:
- The Genomic Threading Database (GTD) is a valuable resource for protein structural annotation.
- Accurate protein structure prediction is crucial for understanding biological function.
Purpose of the Study:
- To describe the Genomic Threading Database (GTD) and its methodology for protein structural assignment.
- To report the performance of the GenTHREADER method in predicting protein folds and residue alignments.
Main Methods:
- Utilized a modified GenTHREADER method for reliable fold recognition.
- Employed grid technology to distribute annotation jobs across multiple processor clusters.
- Deposited predictions in a relational database accessible via a web interface.
Main Results:
- The GTD contains structural assignments for proteins from nine eukaryotes and 101 prokaryotes.
- Up to 84% of proteins in a genome can be confidently assigned to known folds with 72% residue alignment.
- On average, 64% of proteins are assigned to known folds with 58% residue alignment.
Conclusions:
- The GTD system, using GenTHREADER, provides high-confidence structural assignments for a significant proportion of proteins.
- The database and web interface facilitate access to valuable structural annotation data for genomic research.