A protein taxonomy based on secondary structure

Nat Struct Biol. 1999 Jul;6(7):672-82. doi: 10.1038/10728.

Abstract

Does a protein's secondary structure determine its three-dimensional fold? This question is tested directly by analyzing proteins of known structure and constructing a taxonomy based solely on secondary structure. The taxonomy is generated automatically, and it takes the form of a tree in which proteins with similar secondary structure occupy neighboring leaves. Our tree is largely in agreement with results from the structural classification of proteins (SCOP), a multidimensional classification based on homologous sequences, full three-dimensional structure, information about chemistry and evolution, and human judgment. Our findings suggest a simple mechanism of protein evolution.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Animals
  • Classification*
  • Computer Simulation
  • Databases, Factual
  • Evolution, Molecular
  • Protein Folding
  • Protein Structure, Secondary*