Protein structure prediction using sparse dipolar coupling data

Y. Qu
2004 Nucleic Acids Research  
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 15 N± 1 H RDC data of the protein recorded in a single ordering medium.
more » ... 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 15 N± 1 H RDC data (representing 43 proteins) deposited in the BioMagResBank (BMRB) database. The program correctly identi®ed structural folds for 83.7% of the target proteins, and achieved an average alignment accuracy of 98.1% residues within a four-residue shift.
doi:10.1093/nar/gkh204 pmid:14744980 pmcid:PMC373331 fatcat:eoijnj7xhbdq5o2wpsy6rs4czu