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

Abstract

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