M. Leutner et al., AUTOMATED BACKBONE ASSIGNMENT OF LABELED PROTEINS USING THE THRESHOLDACCEPTING ALGORITHM, Journal of biomolecular NMR, 11(1), 1998, pp. 31-43
The sequential assignment of backbone resonances is the first step in
the structure determination of proteins by heteronuclear NMR. For larg
er proteins, an assignment strategy based on proton side-chain informa
tion is no longer suitable for the use in an automated procedure. Our
program PASTA (Protein ASsignment by Threshold Accepting) is therefore
designed to partially or fully automate the sequential assignment of
proteins, based on the analysis of NMR backbone resonances plus C-beta
information. In order to overcome the problems caused by peak overlap
and missing signals in an automated assignment process, PASTA uses th
reshold accepting, a combinatorial optimization strategy, which is sup
erior to simulated annealing due to generally faster convergence and b
etter solutions. The reliability of this algorithm is shown by reprodu
cing the complete sequential backbone assignment of several proteins f
rom published NMR data. The robustness of the algorithm against misass
igned signals, noise, spectral overlap and missing peaks is shown by r
epeating the assignment with reduced sequential information and increa
sed chemical shift tolerances. The performance of the program on real
data is finally demonstrated with automatically picked peak lists of h
uman nonpancreatic synovial phospholipase A(2), a protein with 124 res
idues.