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Bioinformatics, Vol 15, 66-71, Copyright © 1999 by Oxford University Press

ARTICLES

A fast, stochastic threading algorithm for proteins

OH Crawford
Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6480, USA. crawfordoh@ornl.gov

MOTIVATION: Sequences for new proteins are being determined at a rapid rate, as a result of the Human Genome Project, and related genome research. The ability to predict the three-dimensional structure of proteins from sequence alone would be useful in discovering and understanding their function. Threading, or fold recognition, aims to predict the tertiary structure of a protein by aligning its amino acid sequence with a large number of structures, and finding the best fit. This approach depends on obtaining good performance from both the scoring function, which simulates the free energy for given trial alignments, and the threading algorithm, which searches for the lowest- score alignment. It appears that current scoring functions and threading algorithms need improvement. RESULTS: This paper presents a new threading algorithm. Numerical tests demonstrate that it is more powerful than two popular approximate algorithms, and much faster than exact methods.
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This article has been cited by other articles:


Home page
 Protein Eng Des SelHome page
Y. Xu, D. Xu, O. H. Crawford, J.r. Einstein, F. Larimer, E. Uberbacher, M. A. Unseren, and G. Zhang
Protein threading by PROSPECT: a prediction experiment in CASP3
Protein Eng. Des. Sel., November 1, 1999; 12(11): 899 - 907.
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