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Comparison of sequence and structure-based datasets for nonredundant structural data mining.

Carmen K Chu1, Lina L Feng, Merridee A Wouters

  • 1Computational Biology and Bioinformatics Program, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.

Proteins
|July 8, 2005
PubMed
Summary
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Protein Data Bank (PDB) subsets like PDB_SELECT are not fully representative of protein folds. Structural databases SCOP and CATH also have limitations, requiring further work for optimal protein structure analysis.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Structural data mining aims to extract principles from protein structures in the Protein Data Bank (PDB).
  • The complete PDB is not representative of all protein folds, with some being overrepresented and others missing.
  • Existing methods for creating non-redundant datasets, like PDB_SELECT, have limitations.

Purpose of the Study:

  • To compare the representativeness of the PDB_SELECT dataset with structural databases SCOP and CATH.
  • To identify limitations in current methods for generating non-redundant protein structure datasets.
  • To highlight areas for improvement in protein fold representation for data mining.

Main Methods:

  • Comparison of PDB_SELECT dataset (sequence-derived) with SCOP and CATH (structure-derived databases).

Related Experiment Videos

  • Analysis of fold representation and redundancy across the compared datasets.
  • Evaluation of the strengths and weaknesses of each dataset approach.

    • Main Results:

    • The PDB_SELECT dataset still shows overrepresentation of some protein folds and underrepresentation of others.
    • SCOP and CATH databases, while valuable, present challenges such as labor-intensive updates and defining fold distances.
    • Neither sequence-based filtering nor current structural classifications provide a perfectly representative dataset of all protein folds.

    Conclusions:

    • Current methods for curating non-redundant protein structure datasets have inherent limitations.
    • Further research is needed to develop more accurate and comprehensive methods for representing the full diversity of protein folds.
    • Improved datasets are crucial for advancing structural data mining and understanding general principles of protein structure.