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Related Experiment Videos

Sequence-structure mapping errors in the PDB: OB-fold domains.

Ceslovas Venclovas1, Krzysztof Ginalski, Chulhee Kang

  • 1Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, L-448, PO Box 808, Livermore, CA 94551, USA. venclovas@Ilnl.gov

Protein Science : a Publication of the Protein Society
|May 11, 2004
PubMed
Summary
This summary is machine-generated.

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Researchers found sequence-structure mapping errors in Protein Data Bank (PDB) OB-fold structures. Computational methods effectively detected and corrected these errors, improving structural data accuracy.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Chemistry

Background:

  • The Protein Data Bank (PDB) is a crucial resource for structural data of biological molecules.
  • Maintaining accuracy in PDB data, particularly sequence-structure mapping, is essential for reliable research.
  • Oligonucleotide/oligosaccharide binding (OB)-fold structures are prevalent in the PDB.

Purpose of the Study:

  • To identify sequence-structure mapping errors within PDB crystal structures of OB-fold proteins.
  • To evaluate the efficacy of computational methods in detecting and correcting these errors.
  • To demonstrate the practical application of computational analysis in refining PDB entries.

Main Methods:

  • Analysis of PDB crystal structures with OB-folds.

Related Experiment Videos

  • Application of energy-based structure quality assessment.
  • Utilizing sequence analyses in conjunction with structural data.

    • Main Results:

    • At least five OB-structures in the PDB exhibit sequence-structure mapping errors.
    • Computational techniques successfully detected and provided guidance for correcting these errors.
    • A specific PDB entry was revised based on computational findings, and the corrected structure was re-deposited.

    Conclusions:

    • The combination of energy assessment and sequence analysis is effective for detecting sequence-structure mapping errors.
    • These computational approaches can guide the correction of errors in structural data.
    • Implementing these methods can enhance the accuracy of structure determination and verification, especially for poorly defined regions.