Automated NOESY Assignment

The structure of this chapter is as follows Section 2.2 introduces the various types of conformational constraints used in NMR structure calculations. Section 2.3 is devoted to modern structure calculation algorithms. Section 2.4 gives an account of the general principles and the practice of automated NOESY assignment. 

The latest approach to automated NOESY assignment is the Candid algorithm [26], which will be explained in detail in the following sections. 

Semi-automated approaches to NOESY assignment [85-87] use the chemical shifts and a model or preliminary structure to provide the user with the list of possible assignments for each cross peak. The user decides interactively about the assignment and/or temporary removal of individual NOESY cross peaks, possibly taking into account supplementary information such as line shapes or secondary structure data, and performs a structure calculation with the resulting (usually incomplete) input. In practice, several cycles of NOESY assignment and structure calculation are required to obtain a high-quality structure. 

Fig. 2.2 General scheme of automated combined NOESY assignment and structure calculation.

The amount of time required to complete a structure by NMR spectroscopy is difficult to estimate. The assignment of peaks in the various NOESY spectra may require 1 to 3 months, depending on the degree of automation utilized. The actual... 

In addition to providing automated peak picking and computation of the corresponding chemical shift lists, APSY supports automated sequential resonance assignment. Thus, APSY is a valid alternative to related NMR techniques. APSY can be the first step, after sample preparation, in a fully automated process of protein stmcture determination by NMR with successive automated algorithms for the NOESY spectrum analysis and structure calculation. 

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