Published online 26 January 2004
Nucleic Acids Research, 2004, Vol. 32, No. 2 551-561
© 2004 Oxford University Press
Protein structure prediction using sparse dipolar coupling data
Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA and Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
*To whom correspondence should be addressed. Tel: +1 706 542 9762; Fax: +1 706 542 9751; Email: xyn{at}bmb.uga.edu
Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies. However, solving a protein structure using RDC data alone is still a highly challenging problem. We report here a computer program, RDC-PROSPECT, for protein structure prediction based on a structural homolog or analog of the target protein in the Protein Data Bank (PDB), which best aligns with the 15N–1H RDC data of the protein recorded in a single ordering medium. Since RDC-PROSPECT uses only RDC data and predicted secondary structure information, its performance is virtually independent of sequence similarity between a target protein and its structural homolog/analog, making it applicable to protein targets beyond the scope of current protein threading techniques. We have tested RDC-PROSPECT on all 15N–1H RDC data (representing 43 proteins) deposited in the BioMagResBank (BMRB) database. The program correctly identified structural folds for 83.7% of the target proteins, and achieved an average alignment accuracy of 98.1% residues within a four-residue shift.