Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3

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Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3

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NMR processing:

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NMR assignment:

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Side-chains:

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Structure from NMR restraints:

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Rosetta-NMR (Robetta)

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GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

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RCI

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Methyl S2

B-factor

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Shiftx2

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Camshift

CH3shift- Methyl

ArShift- Aromatic

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Proshift

PPM

CheShift-2- Cα

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Shifty

Camcoil

Poulsen_rc_CS

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CCPN

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Protein solubility:

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05-20-2015, 10:27 AM

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Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3

Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3

Abstract

We present an analysis of the results obtained at CASD-NMR round 3 by the CHESHIRE and the YAPP methods. To determine protein structures, the CHESHIRE method uses solely information provided by NMR chemical shifts, while the YAPP method uses an automated assignment of NOESY spectra. Of the ten targets of CASD-NMR round 3, nine CHESHIRE predictions and eight YAPP ones were submitted. The eight YAPP predictions ranged from 0.7 to 1.9 Ã? CÎ± accuracy, with an average of 1.3 Ã?. The nine CHESHIRE predictions ranged from 0.8 to 2.6 Ã? CÎ± accuracy for the ordered regions of the proteins, with an average of 1.6 Ã?. Taken together, these results illustrate how the NOESY based YAPP method and the chemical shift based CHESHIRE method can provide structures of comparable quality.

Source: Journal of Biomolecular NMR

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