Journal of Biomolecular NMR, 12: 395–405, 1998. KLUWER/ESCOM © 1998 Kluwer Academic Publishers. Printed in the Netherlands. 395 CAMRA: Chemical shift based computer aided protein NMR assignments Wolfram Gronwald a,b , Leigh Willard a , Timothy Jellard a , Robert F. Boyko b , Krishna Rajarathnam a,b , David S. Wishart a,c , Frank D. Sönnichsen d and Brian D. Sykes a,b,∗ a Protein Engineering Network of Centres of Excellence, 713 Heritage Medical Research Centre, University of Alberta, Edmonton, AB, Canada T6G 2S2; b Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7; c Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada T6G 2N8; d Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106-4970, U.S.A. Received 26 March 1998; Accepted 8 June 1998 Key words: assignment homology programs, automatic Abstract A suite of programs called CAMRA (Computer Aided Magnetic Resonance Assignment) has been developed for computer assisted residue-specific assignments of proteins. CAMRA consists of three units: ORB, CAPTURE and PROCESS. ORB predicts NMR chemical shifts for unassigned proteins using a chemical shift database of previ- ously assigned homologous proteins supplemented by a statistically derived chemical shift database in which the shifts are categorized according to their residue, atom and secondary structure type. CAPTURE generates a list of valid peaks from NMR spectra by filtering out noise peaks and other artifacts and then separating the derived peak list into distinct spin systems. PROCESS combines the chemical shift predictions from ORB with the spin systems identified by CAPTURE to obtain residue specific assignments. PROCESS ranks the top choices for an assignment along with scores and confidence values. In contrast to other auto-assignment programs, CAMRA does not use any connectivity information but instead is based solely on matching predicted shifts with observed spin systems. As such, CAMRA represents a new and unique approach for the assignment of protein NMR spectra. CAMRA will be particularly useful in conjunction with other assignment methods and under special circumstances, such as the assignment of flexible regions in proteins where sufficient NOE information is generally not available. CAMRA was tested on two medium-sized proteins belonging to the chemokine family. It was found to be effective in predicting the assignment providing a database of previously assigned proteins with at least 30% sequence identity is available. CAMRA is versatile and can be used to include and evaluate heteronuclear and three-dimensional experiments. Abbreviations: CAMRA, Computer Aided Magnetic Resonance Assignment; GUI, graphical user interface; IL-8, interleukin-8; NOE, nuclear Overhauser effect; SDF-1, stromal derived factor-1; IPP, interactive peak picker; SSS, spin system separation. Introduction Nuclear magnetic resonance spectroscopy is widely used for the determination of protein structures in so- lution. However, the time required to solve a new protein NMR structure can vary from months to years, with the residue-specific assignment of the NMR spec- ∗ To whom correspondence should be addressed. tra being the time limiting step. For small or medium- sized proteins the sequential assignment process relies primarily on conventional two-dimensional methods (Wüthrich, 1986). For large proteins, several strate- gies have been proposed for sequence-specific assign- ments, based on the combination of various heteronu- clear experiments using 13 C and 15 N labeled proteins (for reviews see Clore and Gronenborn, 1991 and Bax