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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics
Marcin von Grotthuss1, Dariusz Plewczynski, Krzysztof Ginalski
1Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA. mvg@paradox.harvard.edu
BMC Bioinformatics
|February 8, 2006
Summary
Structural similarity can predict protein function for unannotated proteins. The PDB-UF database aids in assigning enzymatic properties, identifying four hypothetical proteins as methyltransferases.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Increasing protein structures in the Protein Data Bank (PDB) from structural genomics initiatives lead to many functionally unannotated proteins.
- Lack of sequence similarity often hinders functional annotation, despite the potential for inferring function from structural similarity.
Purpose of the Study:
- To present the PDB-UF database, a web-accessible resource for predicting enzymatic properties of proteins with unknown functions.
- To demonstrate the utility of structure-function relationships for annotating proteins from structural genomics.
Main Methods:
- Utilized structure-function relationship analysis to predict enzymatic properties for proteins lacking sequence homology.
- Applied computational methods to analyze three-dimensional protein structures from structural genomics projects.
Main Results:
- The PDB-UF database provides predictions for enzymatic properties based on structural similarity.
- Four hypothetical proteins (1VH0, 1NS5, 1O6D, 1TO0), previously unannotated by standard BLAST tools, were identified as probable methyltransferases.
Conclusions:
- Structure-based prediction of EC numbers should consider protein fold-specific similarity score cutoffs.
- Employing multiple algorithms for annotation can decrease false positive assignments.
- The PDB-UF database aims to reduce the number of proteins with "unknown" function in the PDB.
