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Related Experiment Videos

PKB: a program system and data base for analysis of protein structure.

S H Bryant1

  • 1Chemistry Department, Brookhaven National Laboratory, Upton, New York 11973.

Proteins
|January 1, 1989
PubMed
Summary
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The Protein Knowledge Base (PKB) program system aids in analyzing protein structures and folding patterns. It enables searching structural databases for motifs and examining conformational and electrostatic properties.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Protein structure databases are essential for understanding protein function and folding.
  • Identifying recurring structural motifs aids in predicting protein behavior.
  • Analyzing conformational and electrostatic properties provides insights into protein stability.

Purpose of the Study:

  • To introduce the Protein Knowledge Base (PKB) system for protein structure analysis.
  • To demonstrate PKB's utility in identifying and analyzing structural motifs.
  • To apply PKB to investigate protein folding patterns and related properties.

Main Methods:

  • Utilizing a database of three-dimensional protein structures.
  • Employing algorithms for pattern recognition, data analysis, and graphics.

Related Experiment Videos

  • Executing user-defined searches for structural motifs and detailed analysis of retrieved structures.

    • Main Results:

    • PKB successfully identified and analyzed instances of the Arg-Gly-Asp motif and beta alpha beta units.
    • The system facilitated the examination of ion-pair interactions and their correlation with electrostatic energy.
    • Conformational and sequence similarities were effectively compared using PKB.

    Conclusions:

    • The Protein Knowledge Base (PKB) is a valuable tool for structural bioinformatics research.
    • PKB enhances the ability to study protein folding by analyzing structural motifs and properties.
    • The system supports detailed investigation into sequence-structure relationships and energetic contributions.