ArticleJournal of biomolecular NMR2009
Automated assignment of NMR chemical shifts using peak-particle dynamics simulation with the DYNASSIGN algorithm.
Article in Journal of biomolecular NMR, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
- Evaluation of Multi-Objective Optimization Algorithms for NMR Chemical Shift Assignment.Molecules (Basel, Switzerland) · 2021Article
- Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.Chemistry (Weinheim an der Bergstrasse, Germany) · 2015Article
- APSY-NMR for protein backbone assignment in high-throughput structural biology.Journal of biomolecular NMR · 2015Article
- Automated robust and accurate assignment of protein resonances for solid state NMR.Journal of biomolecular NMR · 2014Article
- Automated and assisted RNA resonance assignment using NMR chemical shift statistics.Nucleic acids research · 2013Article
- Automated solid-state NMR resonance assignment of protein microcrystals and amyloids.Journal of biomolecular NMR · 2013Article
- Prediction of peak overlap in NMR spectra.Journal of biomolecular NMR · 2013Article
- Peakmatch: a simple and robust method for peak list matching.Journal of biomolecular NMR · 2013Article
- The J-UNIO protocol for automated protein structure determination by NMR in solution.Journal of biomolecular NMR · 2012Article
- Comparative NMR analysis of an 80-residue G protein-coupled receptor fragment in two membrane mimetic environments.Biochimica et biophysica acta · 2011Article
- Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm.Journal of biomolecular NMR · 2011Article
- Advances in Nuclear Magnetic Resonance for Drug Discovery.Expert opinion on drug discovery · 2009Article
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Authors and funding
3 authors.
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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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