New Fold Methods:Prediction Reports

Combining local-structure, fold-recognition, and new fold methods for protein structure prediction

  1. Kevin Karplus*,
  2. Rachel Karchin,
  3. Jenny Draper,
  4. Jonathan Casper,
  5. Yael Mandel-Gutfreund,
  6. Mark Diekhans,
  7. Richard Hughey

Article first published online: 15 OCT 2003

DOI: 10.1002/prot.10540

Issue

Proteins: Structure, Function, and Bioinformatics

Proteins: Structure, Function, and Bioinformatics

Supplement: Fifth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction

Volume 53, Issue Supplement 6, pages 491–496, 2003

Additional Information

How to Cite

Karplus, K., Karchin, R., Draper, J., Casper, J., Mandel-Gutfreund, Y., Diekhans, M. and Hughey, R. (2003), Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins, 53: 491–496. doi: 10.1002/prot.10540

Author Information

  1. Computer Engineering Department, University of California, Santa Cruz, California

*Computer Engineering Department, University of California, Santa Cruz, CA 95064

Publication History

  1. Issue published online: 15 OCT 2003
  2. Article first published online: 15 OCT 2003
  3. Manuscript Accepted: 3 APR 2003
  4. Manuscript Received: 3 MAR 2003

Funded by

  • National Science Foundation. Grant Numbers: DBT-9808007 and EIA-9905322, DE-FG0395-99ER62849
  • National Physical Sciences Consortium graduate fellowship

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Keywords:

  • SAM-T02;
  • UNDERTAKER;
  • fragment-packing program;
  • hidden Markov model;
  • secondary structure

Abstract

This article presents an overview of the SAM-T02 method for protein fold recognition and the UNDERTAKER program for ab initio predictions. The SAM-T02 server is an automatic method that uses two-track hidden Markov models (HMMS) to find and align template proteins from PDB to the target protein. The two-track HMMs use an amino acid alphabet and one of several different local structure alphabets. The UNDERTAKER program is a new fragment-packing program that can use short or long fragments and alignments to create protein conformations. The HMMs and fold-recognition alignments from the SAM-T02 method were used to generate the fragment and alignment libraries used by UNDERTAKER. We present results on a few selected targets for which this combined method worked particularly well: T0129, T0181, T0135, T0130, and T0139. Proteins 2003;53:491–496. © 2003 Wiley-Liss, Inc.

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