TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts |
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Authors: | Yang Shen Frank Delaglio Gabriel Cornilescu Ad Bax |
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Institution: | (1) Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA;(2) National Magnetic Resonance Facility, Madison, WI 53706, USA |
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Abstract: | NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between
13C, 15N and 1H chemical shifts and backbone torsion angles ϕ and ψ (Cornilescu et al. J Biomol NMR 13 289–302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles
could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter
to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction
rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly
differ from those observed in the crystalline state, the accuracy of predicted ϕ and ψ angles, equals ±13°. Large discrepancies between predictions and crystal structures are primarily limited to loop regions,
and for the few cases where multiple X-ray structures are available such residues are often found in different states in the
different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the
neural network component of the program also predicts secondary structure with good accuracy.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
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Keywords: | Heteronuclear chemical shift Secondary structure Order parameter Dynamics TALOS |
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