ArticleProtein science : a publication of the Protein Society2012
Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures.
Article in Protein science : a publication of the Protein Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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45 citing papers in PubMed.
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- Xplor-NIH: Better parameters and protocols for NMR protein structure determination.Protein science : a publication of the Protein Society · 2024Article
- Structural basis of protein condensation on microtubules underlying branching microtubule nucleation.Nature communications · 2023Article
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- Divergent self-association properties of paralogous proteins TRIM2 and TRIM3 regulate their E3 ligase activity.Nature communications · 2022Article
- Magic-angle-spinning NMR structure of the kinesin-1 motor domain assembled with microtubules reveals the elusive neck linker orientation.Nature communications · 2022Article
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- The structure of a minimum amyloid fibril core formed by necroptosis-mediating RHIM of human RIPK3.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The amyloid structure of mouse RIPK3 (receptor interacting protein kinase 3) in cell necroptosis.Nature communications · 2021Article
- Atomic-resolution structure of HIV-1 capsid tubes by magic-angle spinning NMR.Nature structural & molecular biology · 2020Article
- Inter-domain dynamics in the chaperone SurA and multi-site binding to its outer membrane protein clients.Nature communications · 2020Article
- A three-dimensional potential of mean force to improve backbone and sidechain hydrogen bond geometry in Xplor-NIH protein structure determination.Protein science : a publication of the Protein Society · 2020Article
- Accuracy and precision of protein structures determined by magic angle spinning NMR spectroscopy: for some 'with a little help from a friend'.Journal of biomolecular NMR · 2019Article
- On the necessity of an integrative approach to understand protein structural dynamics.Journal of Zhejiang University. Science. B · 2019Review
- Characterisation of class VI TRIM RING domains: linking RING activity to C-terminal domain identity.Life science alliance · 2019Article
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Abstract
Statistical potentials that embody torsion angle probability densities in databases of high-quality X-ray protein structures supplement the incomplete structural information of experimental nuclear magnetic resonance (NMR) datasets. By biasing the conformational search during the course of structure calculation toward highly populated regions in the database, the resulting protein structures display better validation criteria and accuracy. Here, a new statistical torsion angle potential is developed using adaptive kernel density estimation to extract probability densities from a large database of more than 10⁶ quality-filtered amino acid residues. Incorporated into the Xplor-NIH software package, the new implementation clearly outperforms an older potential, widely used in NMR structure elucidation, in that it exhibits simultaneously smoother and sharper energy surfaces, and results in protein structures with improved conformation, nonbonded atomic interactions, and accuracy.
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