A protein taxonomy based on secondary structure.
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.
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
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D000465:Algorithms; D000818:Animals; D002965:Classification; D003198:Computer Simulation; D016208:Databases, Factual; D019143:Evolution, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary