ArticleNucleic acids research2012
STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- Core packing of well-defined X-ray and NMR structures is the same.Protein science : a publication of the Protein Society · 2022Article
- Comparative studies of the expression of creatine kinase isoforms under immune stress in Pelodiscus sinensis.International journal of biological macromolecules · 2020Article
- Finding the needle in the haystack: towards solving the protein-folding problem computationally.Critical reviews in biochemistry and molecular biology · 2018Review
- Improving NMR Structures of RNA.Structure (London, England : 1993) · 2016Article
- Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures.Journal of the American Chemical Society · 2014Article
- Protein NMR structures refined without NOE data.PloS one · 2014Article
- Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures.Protein science : a publication of the Protein Society · 2012Article
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6 authors.
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Abstract
According to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. We present a public database of 2405 refined NMR solution structures [statistical torsion angle potentials (STAP) refinement of the NMR database, http://psb.kobic.re.kr/STAP/refinement] from the Protein Data Bank (PDB). A simulated annealing protocol was employed to obtain refined structures with target potentials, including the newly developed STAP. The refined database was extensively analysed using various quality indicators from several assessment programs to determine the nuclear Overhauser effect (NOE) completeness, Ramachandran appearance, χ(1)-χ(2) rotamer normality, various parameters for protein stability and other indicators. Most quality indicators are improved in our protocol mainly due to the inclusion of the newly developed knowledge-based potentials. This database can be used by the NMR structure community for further development of research and validation tools, structure-related studies and modelling in many fields of research.
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