ORB, a homology-based program for the prediction of protein NMR chemical shifts

A computer program (ORB) has been developed to predict H-1, C-13 and N-15 NMR chemical shifts of previously unassigned proteins. The program makes use of the information contained in a chemical shift database of previously assigned proteins supplemented by a statistically derived averaged chemical shift database in which the shifts are categorized according to their residue, atom and secondary structure type [Wishart et al. (1991) J. Mol. Biol., 222, 311-333]. The prediction process starts with a multiple alignment of all previously assigned proteins with the unassigned query protein. ORB uses the sequence and secondary structure alignment program XALIGN for this task [Wishart et al. (1994) CABIOS, 10, 121-132; 687-688]. The prediction algorithm in ORB is based on a scoring of the known shifts for each sequence. The scores depend on global sequence similarity, local sequence similarity, structural similarity and residue similarity and determine how much weight one particular shift is given in the prediction process. In situations where no applicable previously assigned chemical shifts are available, the shifts derived from the averaged database are used, In addition to supplying the user with predicted chemical shifts, ORB calculates a confidence value for every prediction. These confidence values enable the user to judge which predictions are the most accurate and they are particularly useful when ORB is incorporated into a complete autoassignment package. The usefulness of ORB was tested on three medium-sized proteins: an interleukin-8 analog, a troponin C synthetic peptide heterodimer and cardiac troponin C, Excellent results are obtained if ORB is able to use the chemical shifts of al least one highly homologous sequence. ORB performs well as long as the sequence identity between proteins with known chemical shifts and the new sequence is not less than 30%.