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Related Experiment Videos

Targeting novel folds for structural genomics.

Liam J McGuffin1, David T Jones

  • 1Institute of Cancer Genetics and Pharmacogenomics, Department of Biological Sciences, Brunel University, Uxbridge, Middlesex, United Kingdom.

Proteins
|May 16, 2002
PubMed
Summary

Structural genomics aims to determine protein structures for gene function. Simple secondary structure alignments can identify novel protein folds more effectively than existing methods for structural genomics.

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Area of Science:

  • Structural biology
  • Genomics
  • Bioinformatics

Background:

  • Structural genomics aims to determine the 3D structure of all proteins within a genome to understand gene function.
  • Experimental structure determination is costly and time-consuming, making it impractical for all proteins.
  • Comparative modeling and fold recognition methods have limitations in identifying novel protein folds.

Purpose of the Study:

  • To develop and evaluate methods for rapidly and reliably identifying novel protein folds from proteomic data.
  • To expand the available protein fold libraries for structural genomics initiatives.

Main Methods:

  • Analysis of simple methods to discriminate between novel and known protein folds.
  • Comparison of secondary structure element alignments using predicted secondary structures against existing methods like GenTHREADER and standard sequence alignment.

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Main Results:

  • Simple alignments of secondary structure elements show potential as a selective method for identifying novel folds.
  • This approach may be more effective than fold recognition or sequence alignment for proteins with no detectable homology.

Conclusions:

  • Secondary structure element alignment using predicted structures offers a promising strategy for identifying novel protein folds.
  • This method can enhance the efficiency of structural genomics by prioritizing targets for experimental structure determination.