Related ArticlesComputational assignment of protein backbone NMR peaks by efficient bounding and filtering.
J Bioinform Comput Biol. 2003 Jul;1(2):387-409
Authors: Lin G, Xu D, Chen ZZ, Jiang T, Wen J, Xu Y
NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents a new computational method based on the combination of a suite of algorithms for automating the assignment process, particularly the process of backbone resonance peak assignment. We formulate the assignment problem as a constrained weighted bipartite matching problem. While the problem, in the most general situation, is NP-hard, we present an efficient solution based on a branch-and-bound algorithm with effective bounding techniques using two recently introduced approximation algorithms. We also devise a greedy filtering algorithm for reducing the search space. Our experimental results on 70 instances of (pseudo) real NMR data derived from 14 proteins demonstrate that the new solution runs much faster than a recently introduced (exhaustive) two-layer algorithm and recovers more correct peak assignments than the two-layer algorithm. Our result demonstrates that integrating different algorithms can achieve a good tradeoff between backbone assignment accuracy and computation time.
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 4 January 2011</br>
Jie, Wen , Jihui, Wu , Pei, Zhou</br>
Intrinsically disordered proteins (IDPs) play important roles in many critical cellular processes. Due to their limited chemical shift dispersion, IDPs often require four pairs of resonance connectivities (H?, C?, C? and CO) for establishing sequential backbone assignment. Because most conventional 4-D...
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01-05-2011 11:03 AM
RDC derived protein backbone resonance assignment using fragment assembly
RDC derived protein backbone resonance assignment using fragment assembly
Abstract Experimental residual dipolar couplings (RDCs) in combination with structural models have the potential for accelerating the protein backbone resonance assignment process because RDCs can be measured accurately and interpreted quantitatively. However, this application has been limited due to the need for very high-resolution structural templates. Here, we introduce a new approach to resonance assignment based on optimal agreement between the experimental and calculated RDCs from a structural template that...
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12-31-2010 08:38 PM
[NMR paper] Reconsidering complete search algorithms for protein backbone NMR assignment.
Reconsidering complete search algorithms for protein backbone NMR assignment.
Related Articles Reconsidering complete search algorithms for protein backbone NMR assignment.
Bioinformatics. 2005 Sep 1;21 Suppl 2:ii230-6
Authors: Vitek O, Bailey-Kellogg C, Craig B, Kuliniewicz P, Vitek J
MOTIVATION: Nuclear magnetic resonance (NMR) spectroscopy is widely used to determine and analyze protein structures. An essential step in NMR studies is determining the backbone resonance assignment, which maps individual atoms to experimentally measured...
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12-01-2010 06:56 PM
[NMR paper] NMR backbone assignment of the mitogen-activated protein (MAP) kinase p38.
NMR backbone assignment of the mitogen-activated protein (MAP) kinase p38.
Related Articles NMR backbone assignment of the mitogen-activated protein (MAP) kinase p38.
J Biomol NMR. 2005 Jun;32(2):175
Authors: Vogtherr M, Saxena K, Grimme S, Betz M, Schieborr U, Pescatore B, Langer T, Schwalbe H
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11-25-2010 08:21 PM
[NMR paper] An efficient branch-and-bound algorithm for the assignment of protein backbone NMR pe
An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks.
Related Articles An efficient branch-and-bound algorithm for the assignment of protein backbone NMR peaks.
Proc IEEE Comput Soc Bioinform Conf. 2002;1:165-74
Authors: Lin G, Xu D, Chen ZZ, Jiang T, Wen J, Xu Y
NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and...
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11-24-2010 08:49 PM
[NMR paper] An efficient high-throughput resonance assignment procedure for structural genomics a
An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR.
Related Articles An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR.
Biochemistry. 2001 Dec 11;40(49):14727-35
Authors: Bhavesh NS, Panchal SC, Hosur RV
Sequence specific resonance assignment is the primary requirement for all investigations of proteins by NMR methods. In the present postgenomic era where structural genomics and protein folding have...
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11-19-2010 08:44 PM
[NMR paper] A sequential HNCA NMR pulse sequence for protein backbone assignment.
A sequential HNCA NMR pulse sequence for protein backbone assignment.
Related Articles A sequential HNCA NMR pulse sequence for protein backbone assignment.
J Magn Reson. 2001 May;150(1):100-4
Authors: Meissner A, Sørensen OW
The conventional HNCA pulse sequence suffers from the ambiguity that it cannot distinguish inter- and intraresidue correlations because the one-bond and two-bond J(NC(alpha)) coupling constants are of similar magnitude. This paper presents a novel pulse sequence, sequential HNCA, that leads to a spectrum exhibiting...
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11-19-2010 08:32 PM
[NMR paper] An efficient 3D NMR technique for correlating the proton and 15N backbone amide reson
An efficient 3D NMR technique for correlating the proton and 15N backbone amide resonances with the alpha-carbon of the preceding residue in uniformly 15N/13C enriched proteins.
Related Articles An efficient 3D NMR technique for correlating the proton and 15N backbone amide resonances with the alpha-carbon of the preceding residue in uniformly 15N/13C enriched proteins.
J Biomol NMR. 1991 May;1(1):99-104
Authors: Bax A, Ikura M
A 3D NMR technique is described which correlates the amide proton and nitrogen resonances of an amino acid residue...