Research Article

Protein fragment clustering and canonical local shapes

  1. Cornelius G. Hunter1,
  2. Shankar Subramaniam1,2,*

Article first published online: 30 JAN 2003

DOI: 10.1002/prot.10309

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Volume 50, Issue 4, pages 580–588, 1 March 2003

Additional Information

How to Cite

Hunter, C. G. and Subramaniam, S. (2003), Protein fragment clustering and canonical local shapes. Proteins, 50: 580–588. doi: 10.1002/prot.10309

Author Information

  1. 1

    Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Illinois

  2. 2

    Departments of Bioengineering, Chemistry, and Biochemistry, University of California at San Diego, La Jolla, California

*Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093-0412

Publication History

  1. Issue published online: 30 JAN 2003
  2. Article first published online: 30 JAN 2003
  3. Manuscript Accepted: 19 SEP 2002
  4. Manuscript Received: 2 MAY 2002

Funded by

  • National Science Foundation. Grant Numbers: NSF-DBI-9974555, NSF-DBI-0003231

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

View Full Article (HTML) Get PDF (218K)

Keywords:

  • protein structure;
  • protein fragments;
  • local structure;
  • fragment clustering

Abstract

A novel clustering method is used to cluster protein fragments by shape. The centroids (mean fragments from each cluster) form a basis set of structural motifs. A database of 156,643 seven-residue fragments is used, and eight different basis sets with varying levels of resolution are generated. Coarse basis sets contain tens of centroids and provide meaningful local shapes, which are more detailed than the traditional secondary structure categories. High-resolution basis sets contain thousands of centroids and can be used to model tertiary structure of longer segments. The basis sets generated fit nontraining set proteins with the expected accuracy. Proteins 2003;50:580–588. © 2003 Wiley-Liss, Inc.

View Full Article (HTML) Get PDF (218K)