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CADB: Conformation Angles DataBase of proteins.

S S Sheik1, P Ananthalakshmi, G Ramya Bhargavi

  • 1Bioinformatics Centre, Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India.

Nucleic Acids Research
|January 10, 2003
PubMed
Summary

The Conformation Angles DataBase (CADB) offers protein structure data, including main-chain and side-chain angles, aiding in structural analysis. This accessible online resource facilitates the study of amino acid residue conformations and their interrelationships.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational chemistry

Background:

  • Protein structure analysis relies on understanding amino acid residue conformation angles.
  • Databases are crucial for organizing and accessing large-scale structural data.

Purpose of the Study:

  • To introduce the Conformation Angles DataBase (CADB) as a comprehensive online resource.
  • To provide access to protein main-chain and side-chain conformation angle data.
  • To facilitate the study of interrelationships between these angles.

Main Methods:

  • Data compilation from the Protein Data Bank into two sets based on sequence identity (25% and 90%).
  • Inclusion of crystallographic parameters for each protein structure.
  • Development of a web-based JAVA graphics interface for data visualization and analysis.

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Main Results:

  • CADB offers readily accessible data on protein conformation angles for diverse structural studies.
  • Flexible visualization tools allow detailed examination of main-chain and side-chain angles for specific residues.
  • The database supports investigations into the correlations between different types of conformation angles.

Conclusions:

  • CADB serves as a valuable, regularly updated resource for researchers in structural biology and bioinformatics.
  • The database enhances the study of protein structure by providing specialized conformation data and analysis tools.
  • The web interface ensures user-friendly access and visualization of complex structural information.