NMR paper Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality a

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[NMR paper] Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality a

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NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

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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

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

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Chemical shifts:

RDCs:

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SAVES2 or SAVES4

Quality Control Check

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Methyl S2

B-factor

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Shiftx2

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ArShift- Aromatic

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PPM

CheShift-2- Cα

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Camcoil

Poulsen_rc_CS

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MAXOCC

Format conversion & validation:

CCPN

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DisMeta

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11-24-2010, 11:14 PM

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Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality a

Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.

Related Articles Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics.

J Am Chem Soc. 2005 Feb 16;127(6):1665-74

Authors: Huang YJ, Powers R, Montelione GT

One of the most important challenges in modern protein NMR is the development of fast and sensitive structure quality assessment measures that can be used to evaluate the "goodness-of-fit" of the 3D structure with NOESY data, to indicate the correctness of the fold and accuracy of the resulting structure. Quality assessment is especially critical for automated NOESY interpretation and structure determination approaches. This paper describes new NMR quality assessment scores, including Recall, Precision, and F-measure scores (referred to here are "NMR RPF" scores), which quickly provide global measures of the goodness-of-fit of the 3D structures with NOESY peak lists using methods from information retrieval statistics. The sensitivity of the F-measure is improved using a scaled Fold Discriminating Power (DP) score. These statistical RPF scores are quite rapid to compute since NOE assignments and complete relaxation matrix calculations are not required. A graphical method for site-specific assessment of structure quality based on the Precision statistic is also described. These statistical measures are demonstrated to be valuable for assessing protein NMR structure accuracy. Their relationships to other proposed NMR "R-factors" and structure quality assessment scores are also discussed.

PMID: 15701001 [PubMed - indexed for MEDLINE]

Source: PubMed

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