TOOLS FOR THE AUTOMATED ASSIGNMENT OF HIGH-RESOLUTION 3-DIMENSIONAL PROTEIN NMR-SPECTRA BASED ON PATTERN-RECOGNITION TECHNIQUES

One of the major bottlenecks in the determination of protein structure s 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 t he 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 pattern s 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, whi ch 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 f or combinatorial routines, such as sequential assignment procedures, i n place of peak lists. Two examples are presented, in which (i) HCCH-C OSY and -TOCSY spectra are scanned for side-chain spin systems; and (i i) backbone spin systems are detected in a set of spectra comprising H NCA, HN(CO)CA, HNCO, HN(CA)CO, CBCANH and CBCA(CO)NH.