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Related Experiment Videos

Touring protein fold space with Dali/FSSP

L Holm1, C Sander

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute, Genome Campus, Cambridge CB10 1SD, UK. holm@embl-ebi.ac.uk

Nucleic Acids Research
|February 21, 1998
PubMed
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The Dali/FSSP database classifies 3D protein structures using automatic alignment. This provides a map of protein structures for analyzing folding principles and protein family evolution.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure classification

Background:

  • The Protein Data Bank contains a vast number of 3D protein structures.
  • A systematic classification of these structures is needed for analysis and understanding.
  • Existing methods may not fully capture the continuous nature of protein fold space.

Purpose of the Study:

  • To present a continuously updated classification of all known 3D protein structures.
  • To provide a comprehensive resource for analyzing protein folding principles and evolution.
  • To develop a discrete fold classification from continuous structural data.

Main Methods:

  • Utilizing the Dali automatic structure alignment program for all-against-all comparison of Protein Data Bank structures.

Related Experiment Videos

  • Deriving a discrete fold classification through a three-step process: representative sets, domain decomposition, and fold definition.
  • Decomposing protein chains into structural domains based on recurring structural motifs.

    • Main Results:

    • The Dali/FSSP database and Dali Domain Dictionary offer a continuously updated classification of 3D protein structures.
    • Structural neighbors form a continuous distribution in fold space, enabling discrete fold classification.
    • A web interface provides extensive links between related structures, domains, and sequences.

    Conclusions:

    • The Dali/FSSP classification provides a valuable map of protein structure space.
    • This resource aids in understanding protein folding principles and the evolutionary relationships of protein families.
    • It enhances the utility of experimental structure determination by providing context and comparative analysis.