ArticleJournal of biomolecular NMR2002
Automated assignment of NOESY NMR spectra using a knowledge based method (KNOWNOE).
Article in Journal of biomolecular NMR, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Modern Technologies of Solution Nuclear Magnetic Resonance Spectroscopy for Three-dimensional Structure Determination of Proteins Open Avenues for Life Scientists.Computational and structural biotechnology journal · 2017Review
- Non-Uniform Sampling and J-UNIO Automation for Efficient Protein NMR Structure Determination.Chemistry (Weinheim an der Bergstrasse, Germany) · 2015Article
- Combined automated NOE assignment and structure calculation with CYANA.Journal of biomolecular NMR · 2015Article
- Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA.Journal of biomolecular NMR · 2015Article
- Selective diagonal-free (13)C, (13)C-edited aliphatic-aromatic NOESY experiment with non-uniform sampling.Journal of biomolecular NMR · 2013Article
- Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data.Journal of biomolecular NMR · 2011Article
- The interaction of ammonia and xenon with the imidazole glycerol phosphate synthase from Thermotoga maritima as detected by NMR spectroscopy.Protein science : a publication of the Protein Society · 2010Article
- NMR solution structure of human cannabinoid receptor-1 helix 7/8 peptide: candidate electrostatic interactions and microdomain formation.Biochemical and biophysical research communications · 2009Article
- High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations.Journal of biomolecular NMR · 2009Article
- Structural biology of human cannabinoid receptor-2 helix 6 in membrane-mimetic environments.Biochemical and biophysical research communications · 2009Article
- Chemical shift optimization in multidimensional NMR spectra by AUREMOL-SHIFTOPT.Journal of biomolecular NMR · 2009Article
- Automated structure determination from NMR spectra.European biophysics journal : EBJ · 2009Review
- Graphical interpretation of Boolean operators for protein NMR assignments.Journal of biomolecular NMR · 2008Article
- The war of tools: how can NMR spectroscopists detect errors in their structures?Journal of biomolecular NMR · 2008Article
- A global analysis of NMR distance constraints from the PDB.Journal of biomolecular NMR · 2007Article
- AUREMOL-RFAC-3D, combination of R-factors and their use for automated quality assessment of protein solution structures.Journal of biomolecular NMR · 2007Article
- Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data.Journal of biomolecular NMR · 2005Article
- High-temperature solution NMR structure of TmCsp.Protein science : a publication of the Protein Society · 2004Article
- Fully automated sequence-specific resonance assignments of hetero- nuclear protein spectra.Journal of biomolecular NMR · 2003Article
- Automated protein fold determination using a minimal NMR constraint strategy.Protein science : a publication of the Protein Society · 2003Article
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9 authors.
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Abstract
Automated assignment of NOESY spectra is a prerequisite for automated structure determination of biological macromolecules. With the program KNOWNOE we present a novel, knowledge based approach to this problem. KNOWNOE is devised to work directly with the experimental spectra without interference of an expert. Besides making use of routines already implemented in AUREMOL, it contains as a central part a knowledge driven Bayesian algorithm for solving ambiguities in the NOE assignments. These ambiguities mainly arise from chemical shift degeneration which allows multiple assignments of cross peaks. Using a set of 326 protein NMR structures, statistical tables in the form of atom-pairwise volume probability distributions (VPDs) were derived. VPDs for all assignment possibilities relevant to the assignments of interproton NOEs were calculated. With these data for a given cross peak with N possible assignments Ai (i = 1,...,N) the conditional probabilities P(Ai, a/V0) can be calculated that the assignment Ai determines essentially all (a-times) of the cross peak volume V0. An assignment Ak with a probability P(Ak, a/V0) higher than 0.8 is transiently considered as unambiguously assigned. With a list of unambiguously assigned peaks a set of structures is calculated. These structures are used as input for a next cycle of iteration where a distance threshold Dmax is dynamically reduced. The program KNOWNOE was tested on NOESY spectra of a medium size protein, the cold shock protein (TmCsp) from Thermotoga maritima. The results show that a high quality structure of this protein can be obtained by automated assignment of NOESY spectra which is at least as good as the structure obtained from manual data evaluation.
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