ArticleProteins2014
The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 24 citations in OpenAlex.
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- Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2023Article
- Blind Assessment of Monomeric AlphaFold2 Protein Structure Models with Experimental NMR Data.bioRxiv : the preprint server for biology · 2023Article
- AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.Frontiers in molecular biosciences · 2022Article
- Assessment of prediction methods for protein structures determined by NMR in CASP14: Impact of AlphaFold2.Proteins · 2021Article
- Patterns in Protein Flexibility: A Comparison of NMR "Ensembles", MD Trajectories, and Crystallographic B-Factors.Molecules (Basel, Switzerland) · 2021Article
- 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
- A community resource of experimental data for NMR / X-ray crystal structure pairs.Protein science : a publication of the Protein Society · 2016Review
- Guiding automated NMR structure determination using a global optimization metric, the NMR DP score.Journal of biomolecular NMR · 2015Article
- Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.Structure (London, England : 1993) · 2015Article
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- Quality assessment of protein NMR structures.Current opinion in structural biology · 2013Review
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
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.
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