Conditions for unique graph realizations
SIAM Journal on Computing
Reconstructing a three-dimensional model with arbitrary errors
Journal of the ACM (JACM)
Computing in Science and Engineering
Approximation algorithms for NMR spectral peak assignment
Theoretical Computer Science
An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
An Algebraic Geometry Approach to Protein Structure Determination from NMR Data
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Protein loop closure using orientational restraints from NMR data
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
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Nuclear Overhauser effect (NOE) distance restraints are the main experimental data from protein nuclear magnetic resonance (NMR) spectroscopy for computing a complete three dimensional solution structure including sidechain conformations. In general, NOE restraints must be assigned before they can be used in a structure determination program. NOE assignment is very time-consuming to do manually, challenging to fully automate, and has become a key bottleneck for high-throughput NMR structure determination. The difficulty in automated NOE assignment is ambiguity: there can be tens of possible different assignments for an NOE peak based solely on its chemical shifts. Previous automated NOE assignment approaches rely on an ensemble of structures, computed from a subset of all the NOEs, to iteratively filter ambiguous assignments. These algorithms are heuristic in nature, provide no guarantees on solution quality or running time, and are slow in practice. In this paper we present an accurate, efficient NOE assignment algorithm. The algorithm first invokes the algorithm in [30, 29] to compute an accurate backbone structure using only two backbone residual dipolar couplings (RDCs) per residue. The algorithm then filters ambiguous NOE assignments by merging an ensemble of intra-residue vectors from a protein rotamer database, together with internuclear vectors from the computed backbone structure. The protein rotamer database was built from ultra-high resolution structures (