Benchmarking NMR experiments: a relational database of protein pulse sequences

Senthamarai, Russell R.P., Kuprov, Ilya and Pervushin, Konstantin (2010) Benchmarking NMR experiments: a relational database of protein pulse sequences. Journal of Magnetic Resonance, 203, (1), 129-137. (doi:10.1016/j.jmr.2009.12.008).


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Systematic benchmarking of multi-dimensional protein NMR experiments is a critical prerequisite for optimal allocation of NMR resources for structural analysis of challenging proteins, e.g. large proteins with limited solubility or proteins prone to aggregation. We propose a set of benchmarking parameters for essential protein NMR experiments organized into a lightweight (single XML file) relational database (RDB), which includes all the necessary auxiliaries (waveforms, decoupling sequences, calibration tables, setup algorithms and an RDB management system). The database is interfaced to the Spinach library (, which enables accurate simulation and benchmarking of NMR experiments on large spin systems. A key feature is the ability to use a single user-specified spin system to simulate the majority of deposited solution state NMR experiments, thus providing the (hitherto unavailable) unified framework for pulse sequence evaluation. This development enables predicting relative sensitivity of deposited implementations of NMR experiments, thus providing a basis for comparison, optimization and, eventually, automation of NMR analysis. The benchmarking is demonstrated with two proteins, of 170 amino acids I domain of ?X?2 Integrin and 440 amino acids NS3 helicase.

Item Type: Article
Digital Object Identifier (DOI): doi:10.1016/j.jmr.2009.12.008
ISSNs: 1090-7807 (print)
1096-0856 (electronic)
Related URLs:
Subjects: Q Science > QD Chemistry
Divisions : Faculty of Natural and Environmental Sciences > Chemistry > Computational Systems Chemistry
ePrint ID: 337125
Accepted Date and Publication Date:
23 December 2009Made publicly available
Date Deposited: 19 Apr 2012 13:49
Last Modified: 31 Mar 2016 14:26

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