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Related Experiment Videos

Evaluating protein structures determined by structural genomics consortia.

Aneerban Bhattacharya1, Roberto Tejero, Gaetano T Montelione

  • 1Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers University and Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.

Proteins
|December 23, 2006
PubMed
Summary
This summary is machine-generated.

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The Protein Structure Validation Software Suite (PSVS) assesses protein structure quality from NMR and X-ray crystallography. PSVS reveals a quality gap between NMR and X-ray structures, with most NMR structures scoring lower.

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Structural genomics projects generate vast amounts of 3D protein structural data.
  • Accurate assessment of protein structure quality is crucial for biological interpretation.
  • Existing validation tools are numerous and sometimes disparate.

Purpose of the Study:

  • To develop and present the Protein Structure Validation Software Suite (PSVS) for comprehensive protein structure quality assessment.
  • To integrate multiple established validation tools into a single, user-friendly interface.
  • To analyze and compare the quality of protein structures generated by different methods, particularly NMR and X-ray crystallography.

Main Methods:

  • PSVS integrates established tools: PROCHECK, MolProbity, Verify3D, ProsaII, and PDB validation software.

Related Experiment Videos

  • The suite performs constraint analyses, goodness-of-fit assessments, and knowledge-based scoring.
  • Global quality is measured using Z scores calibrated against high-resolution X-ray structures.

    • Main Results:

    • PSVS provides both global and site-specific measures of protein structure quality.
    • Analysis of structures from structural genomics projects shows quality score distributions similar to traditional projects.
    • A notable "structure quality score gap" exists, with most NMR structures scoring lower than X-ray crystal structures.

    Conclusions:

    • PSVS is a valuable tool for assessing protein structures from NMR, X-ray crystallography, and homology modeling.
    • The identified quality gap between NMR and X-ray structures warrants further investigation into underlying causes.
    • PSVS facilitates standardized quality assessment for large-scale structural biology initiatives.