PDB-UF

PDB-UF is a web-accessible database that provides predictions of enzymatic properties using structure-function relationship for functionally unannotated protein structures in the Protein Data Bank (PDB) that lack sequence similarity to proteins of known function. The database can infer function using only structural similarity and suggests that structure-based prediction of an EC number should be conducted with different similarity score cutoffs for different protein folds. PDB-UF can reduce the rate of false positive assignments and decrease the number of protein structures with unknown functions in the PDB file.

Topic

database management; protein structure analysis; enzyme prediction; structure-based function prediction; protein annotation; protein function prediction

Detail

  • Operation: Predictive functional annotation ; Database search and retrieval ; Sequence analysis ; Structural analysis ; Structural classification and folding ; Protein structure analysis ; Enzyme function prediction

  • Software interface: -

  • Language: -

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: The Foundation for Polish Science, 6FP GeneFun and Data Genome grants and by the Polish Ministry of Science and Information.

  • Input: -

  • Output: -

  • Contact: eugene@belok.harvard.edu

  • Collection: -

  • Maturity: Stable

Publications

  • PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
  • von Grotthuss M, et al. PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics. 2006; 7:53. doi: 10.1186/1471-2105-7-53
  • https://doi.org/10.1186/1471-2105-7-53
  • PMID: 16460560
  • PMC: PMC1409798

Download and documentation

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