Tools for the automated assignment of high-resolution three-dimensional protein NMR spectra based on pattern recognition techniques

One of the major bottlenecks in the determination of protein structures by NMR is in the evaluation of the data produced by the experiments. An important step in this process is assignment, where the peaks in the spectra are assigned to specific spins within specific residues. In this paper, we discuss a spin system assignment tool based on pattern recognition techniques. This tool employs user-specified 'templates' to search for patterns of peaks in the original spectra; these patterns may correspond to sidechain or backbone fragments. Multiple spectra will normally be searched simultaneously to reduce the impact of noise. The search generates a preliminary list of putative assignments, which are filtered by a set of heuristic algorithms to produce the final results list. Each result contains a set of chemical shift values plus information about the peaks found. The results may be used as input for combinatorial routines, such as sequential assignment procedures, in place of peak lists. Two examples are presented, in which (i) HCCH-COSY and -TOCSY spectra are scanned for side-chain spin systems; and (ii) backbone spin systems are detected in a set of spectra comprising HNCA, HN(CO)CA, HNCO, HN(CA)CO, CBCANH and CBCA(CO)NH.