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The FSSP database: fold classification based on structure-structure alignment of proteins

L Holm1, C Sander

  • 1European Molecular Biology Laboratory, Heidelberg, Germany.

Nucleic Acids Research
|January 1, 1996
PubMed
Summary

The FSSP database classifies 3-D protein folds using structural comparisons from the Protein Data Bank (PDB). It provides alignments and a fold tree for understanding protein structure relationships.

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Area of Science:

  • Structural bioinformatics
  • Protein structure classification

Background:

  • The Protein Data Bank (PDB) is a crucial resource for 3-D protein structures.
  • Classifying protein folds aids in understanding protein function and evolution.

Purpose of the Study:

  • To present the FSSP database, a continuously updated classification of 3-D protein folds.
  • To provide a comprehensive resource for exploring structural relationships among proteins.

Main Methods:

  • All-against-all comparison of protein structures from the PDB.
  • Utilizing the Dali program for automatic 3-D coordinate-based structure alignment.
  • Hierarchical clustering to generate a fold tree representing structural relationships.

Main Results:

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  • The FSSP database includes 600 representative protein chains with <25% sequence identity.
  • Provides pairwise structure comparisons, fold trees, and structurally representative sets of folds.
  • Database entries contain structure-structure alignments with neighbors and sequence homologs.

Conclusions:

  • The FSSP database offers a valuable, accessible resource for protein structure analysis.
  • Facilitates the study of protein fold families and evolutionary relationships.
  • Accessible via the World Wide Web and anonymous FTP for broad scientific use.