2006
DOI: 10.1089/cmb.2006.13.1267
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A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data

Abstract: We describe an efficient algorithm for protein backbone structure determination from solution Nuclear Magnetic Resonance (NMR) data. A key feature of our algorithm is that it finds the conformation and orientation of secondary structure elements as well as the global fold in polynomial time. This is the first polynomial-time algorithm for de novo high-resolution biomacromolecular structure determination using experimentally recorded data from either NMR spectroscopy or X-ray crystallography. Previous algorithm… Show more

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Cited by 27 publications
(97 citation statements)
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“…Our approach computed all the correct side-chain conformations in core residues for GB1 and FF2, and had accuracies ‡ 84% for ubiquitin, given the backbone structures from the NMR reference structures ( Table 1). The tests on the RDC-defined backbones exhibited similar results (Table 2), which indicates that our current Bayesian approach can be combined with our previously-developed backbone structure determination techniques (Donald and Martin, 2009;Wang and Donald, 2004;Wang et al, 2006;Zeng et al, 2009;Yershova et al, 2011) to determine high-resolution protein structures mainly using RDC and unassigned NOESY data. We also examined the accuracies of the determined side-chain conformations for side-chain amino acid residues of different lengths (Fig.…”
Section: Accuracy Of Determined Side-chain Rotamer Conformationssupporting
confidence: 56%
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“…Our approach computed all the correct side-chain conformations in core residues for GB1 and FF2, and had accuracies ‡ 84% for ubiquitin, given the backbone structures from the NMR reference structures ( Table 1). The tests on the RDC-defined backbones exhibited similar results (Table 2), which indicates that our current Bayesian approach can be combined with our previously-developed backbone structure determination techniques (Donald and Martin, 2009;Wang and Donald, 2004;Wang et al, 2006;Zeng et al, 2009;Yershova et al, 2011) to determine high-resolution protein structures mainly using RDC and unassigned NOESY data. We also examined the accuracies of the determined side-chain conformations for side-chain amino acid residues of different lengths (Fig.…”
Section: Accuracy Of Determined Side-chain Rotamer Conformationssupporting
confidence: 56%
“…The backbone structures were determined by using mainly residual dipolar coupling (RDC) data (Wang and Donald, 2004;Wang et al, 2006;Donald and Martin, 2009), which provides global orientational restraints on the internuclear bond vectors. hana does not completely exploit prior information, nor all the available information from experimental data.…”
Section: Related Workmentioning
confidence: 99%
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