The Expanded FindCore Method for Identification of a Core Atom Set for Assessment of Protein Structure Prediction
By David A. Snyder, Jennifer Grullon, Yuanpeng Janet Huang, R. Tejero, Gaetano T. Montelione. 2014
18 citations recorded by the source corpus.
Maximizing the scientific impact of NMR‐based structure determination requires robust and statistically sound methods for assessing the precision of NMR‐derived structures. In particular, a method to define a core atom set for calculating superimpositions and validating structure predictions is critical to the use of NMR‐derived structures as targets in the CASP competition. FindCore (Snyder and Montelione, Proteins 2005;59:673–686) is a superimposition independent method for identifying a core atom set and partitioning that set into domains. However, as FindCore optimizes superimposition by sensitively excluding not‐well‐defined atoms, the FindCore core may not comprise all atoms suitable for use in certain applications of NMR structures, including the CASP assessment process. Adapting the FindCore approach to assess predicted models against experimental NMR structures in CASP10 required modification of the FindCore method. This paper describes conventions and a standard protocol to calculate an “Expanded FindCore” atom set suitable for validation and application in biological and biophysical contexts. A key application of the Expanded FindCore method is to identify a core set of atoms in the experimental NMR structure for which it makes sense to validate predicted protein structure models. We demonstrate the application of this Expanded FindCore method in characterizing well‐defined regions of 18 NMR‐derived CASP10 target structures. The Expanded FindCore protocol defines “expanded core atom sets” that match an expert's intuition of which parts of the structure are sufficiently well defined to use in assessing CASP model predictions. We also illustrate the impact of this analysis on the CASP GDT assessment scores. Proteins 2014; 82(Suppl 2):219–230. © 2013 Wiley Periodicals, Inc.
Subfields: Materials Chemistry, Molecular Biology
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In Materials Chemistry
- Gaetano T. Montelione
- Binchen Mao
- Yuanpeng Janet Huang
- J. Aramini
- Oliver F. Lange
- Andriy Kryshtafovych
- Krzysztof Fidelis
- John Moult
In Molecular Biology
- Gaetano T. Montelione
- Binchen Mao
- Yuanpeng Janet Huang
- J. Aramini
- Oliver F. Lange
- Nikolaos G. Sgourakis
- Andriy Kryshtafovych
- Krzysztof Fidelis
Citations in the corpus
- Assessment of template based protein structure predictions in CASP10 (2014, methodology): “…as outlined in the accompanying article by Taylor et al .17 Experimental NMR structures, as well as some X-ray crystal structures, were trimmed back to include only the consistently well-defined regions of the structure using the expanded FindCore algorithm, as described by Snyder et al .18”
- Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop (2015, unknown): “Other early examples include the model of the Gla-EGF domains from coagulation Factor X based on NMR and SAS data (Sunnerhagen et al., 1996), and the superhelical assembly of the bacteriophage fd gene 5 protein with single-stranded DNA based on neutron”