Computer-assisted assignment of 2D 1H NMR spectra of proteins: basic algorithms and application to phoratoxin B

Journal/Book: J-Biomol-NMR 1 (1), 23-47. 1991;

Abstract: A suite of computer programs (CLAIRE) is described which can be ofassistance in the process of assigning 2D 1H NMR spectra of proteins.The programs embody a software implementation of the sequentialassignment approach first developed by Wuthrich and co-workers (K.Wuthrich, G. Wider, G. Wagner and W. Braun (1982) J. Mol. Biol. 155,311). After data-abstraction (peakpicking), the software can be used todetect patterns (spin systems), to find cross peaks between patterns in2D NOE data sets and to generate assignments that are consistent withall available data and which satisfy a number of constraints imposed bythe user. An interactive graphics program called CONPAT is used tocontrol the entire assignment process as well as to provide theessential feedback from the experimental NMR spectra. The algorithms aredescribed in detail and the approach is demonstrated on a set of spectrafrom the mistletoe protein phoratoxin B, a homolog of crambin. Theresults obtained compare well with those reported earlier based entirelyon a manual assignment process. Author.

Keyword(s): ALGORITHMS/

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