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Updated: Jun 27, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
Published on: September 17, 2017
Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm
Roland Schmucki1, Shigeyuki Yokoyama, Peter Güntert
1Institute of Biophysical Chemistry and Frankfurt Institute for Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
Abstract:
A new algorithm, DYNASSIGN, for the automated assignment of NMR chemical shift resonances was developed in which expected cross peaks in multidimensional NMR spectra are represented by peak-particles and assignment restraints are translated into a potential energy function. Molecular dynamics simulation techniques are used to calculate a trajectory of the system of peak-particles subjected to the potential function in order to find energetically optimal configurations that correspond to correct assignments. Peak-particle dynamics-based simulated annealing was combined with the Hungarian algorithm for local optimization, and a residue-based score was introduced to distinguish between reliable assignments and "unassigned" resonances for which no reliable assignment can be established. The DYNASSIGN algorithm was implemented in the program CYANA and tested with data sets obtained from the experimental NMR data of nine small proteins. With a set of 10 commonly used NMR spectra, on average 82.5% of all backbone and side-chain (1)H, (13)C and (15)N resonances could be assigned with an average error rate of 3.5%.
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