ArticleProceedings of the National Academy of Sciences of the United States of America2012
Accurate protein structure modeling using sparse NMR data and homologous structure information.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 41 citations in OpenAlex.
- Recent Advances in NMR Protein Structure Prediction with ROSETTA.International journal of molecular sciences · 2023Review
- Chemical shift transfer: an effective strategy for protein NMR assignment with ARTINA.Frontiers in molecular biosciences · 2023Article
- Computational models in the service of X-ray and cryo-electron microscopy structure determination.Proteins · 2021Article
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
- Protein structure prediction using sparse NOE and RDC restraints with Rosetta in CASP13.Proteins · 2019Article
- CS-ROSETTA.Methods in enzymology · 2019Article
- Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra.Nature communications · 2018Article
- Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities.Journal of chemical theory and computation · 2017Article
- Article
- The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data.Journal of biomolecular NMR · 2016Article
- Computational methods in drug discovery.Beilstein journal of organic chemistry · 2016Review
- A community resource of experimental data for NMR / X-ray crystal structure pairs.Protein science : a publication of the Protein Society · 2016Review
- Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis.eLife · 2015Article
- A robust algorithm for optimizing protein structures with NMR chemical shifts.Journal of biomolecular NMR · 2015Article
- Homology modeling of larger proteins guided by chemical shifts.Nature methods · 2015Article
- The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013.Journal of biomolecular NMR · 2015Article
- Consistent global structures of complex RNA states through multidimensional chemical mapping.eLife · 2015Article
- Intrinsic disorder drives N-terminal ubiquitination by Ube2w.Nature chemical biology · 2015Article
- Computational modeling of membrane proteins.Proteins · 2015Review
- A mechanism for the auto-inhibition of hyperpolarization-activated cyclic nucleotide-gated (HCN) channel opening and its relief by cAMP.The Journal of biological chemistry · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 4 institutions in 1 country.
Funding
Abstract
While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.