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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), pp. 129-137. (doi:10.1016/j.jmr.2009.12.008).

Record type: Article

Abstract

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 (http://spindynamics.org), 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.

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More information

e-pub ahead of print date: 23 December 2009
Published date: 2010
Organisations: Computational Systems Chemistry

Identifiers

Local EPrints ID: 337125
URI: http://eprints.soton.ac.uk/id/eprint/337125
PURE UUID: 1bfa7c3e-acfc-4539-b96e-34ae0d70f25e

Catalogue record

Date deposited: 19 Apr 2012 13:49
Last modified: 18 Jul 2017 06:04

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Contributors

Author: Russell R.P. Senthamarai
Author: Ilya Kuprov
Author: Konstantin Pervushin

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