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HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif
C Ferrer-Costa1, H P Shanahan, S Jones
1Molecular Modelling and Bioinformatics, IRBB-Parc Cientific de Barcelona, UB, Josep Samitier, 1-5 08028 Barcelona, Catalonia, Spain.
Bioinformatics (Oxford, England)
|July 21, 2005
Summary
HTHquery is a web tool that identifies helix-turn-helix (HTH) motifs in protein structures, which are crucial for DNA binding. This service aids scientists in predicting DNA-binding capabilities based on structural similarity and electrostatic properties.
Area of Science:
- Structural bioinformatics
- Molecular biology
- Genomics
Background:
- The helix-turn-helix (HTH) motif is a common DNA-binding structure in proteins.
- Identifying HTH motifs is essential for understanding gene regulation and protein function.
Purpose of the Study:
- To develop and present HTHquery, a web-based service for detecting HTH structural motifs in protein structures.
- To provide a user-friendly tool for bench-based scientists to predict DNA-binding potential.
Main Methods:
- HTHquery utilizes structural template similarity, motif accessibility, and electrostatic potential analysis.
- A linear predictor, trained on a dataset, computes similarity scores based on structural templates.
Main Results:
- The HTHquery predictor achieved a high true positive rate of 83.5%.
- The predictor demonstrated a low false positive rate of 0.8% on the training set.
Conclusions:
- HTHquery is an effective web service for identifying potential DNA-binding HTH motifs in protein structures.
- The tool offers a straightforward interface for accessible use by researchers in molecular biology.