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ProTarget: automatic prediction of protein structure novelty.
1School of Computer Science and Engineering, Institute of Life Sciences, Hebrew University of Jerusalem, 91904 Israel.
Nucleic Acids Research
|June 28, 2005
Summary
ProTarget is a web tool that predicts protein fold novelty. It helps select targets for structural genomics by analyzing sequences against known structures to identify new protein superfamilies.
Area of Science:
- Structural biology
- Bioinformatics
Background:
- Structural genomics aims to determine the 3D structures of all proteins.
- Identifying novel protein folds is crucial for understanding protein function and evolution.
- Efficient methods are needed to analyze new protein sequences for structural novelty.
Purpose of the Study:
- To introduce ProTarget, a web-based tool for predicting protein fold novelty.
- To provide a method for target selection in structural genomics.
- To enable online analysis of protein sequences for their relationship to known 3D structures.
Main Methods:
- ProTarget accepts an amino acid sequence as input.
- Regions with high similarity to existing Protein Data Bank (PDB) sequences are identified and removed.
- Remaining subsequences are analyzed against a protein space clustering to determine the likelihood of representing a new structural superfamily based on distance metrics.
Main Results:
- ProTarget provides a graphical visualization of the protein of interest.
- The tool outputs the likelihood of a protein sequence representing a novel structural superfamily.
- The ProTarget database is regularly updated and currently includes over 160,000 protein sequences from SwissProt and PDB.
Conclusions:
- ProTarget offers an automated method for predicting protein fold novelty.
- The tool facilitates target selection for structural genomics projects.
- ProTarget is a valuable resource for researchers investigating protein structure and evolution.