ArticleThe open biochemistry journal2010
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Article in The open biochemistry journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed.
- Interactions of Cyclic Peptides Ribifolin and Gramicidin S with Montmorillonite Surface by Molecular Modeling.ACS omega · 2026Article
- Crystal structures of PF1765 from Pyrococcus furiosus from several different crystallization conditions with varied pH, salt and precipitant.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Exploration of questionable backbone conformations in crystallographic structure models using a structural alphabet.Acta crystallographica. Section D, Structural biology · 2025Article
- Arginine: II. Interactions of Its Salt Bridges with Branched Aliphatic Side Chains.The journal of physical chemistry. B · 2025Article
- Structure-Function Diversity of Calcium-Binding Proteins (CaBPs): Key Roles in Cell Signalling and Disease.Cells · 2025Review
- The homeodomain regulates stable DNA binding of prostate cancer target ONECUT2.Nature communications · 2024Article
- AlphaFold two years on: Validation and impact.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- Interpretation of Hydrogen/Deuterium Exchange Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2024Article
- Easy Not Easy: Comparative Modeling with High-Sequence Identity Templates.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Core packing of well-defined X-ray and NMR structures is the same.Protein science : a publication of the Protein Society · 2022Article
- Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography.Methods in molecular biology (Clifton, N.J.) · 2022Article
- An Integrative Approach to Determine 3D Protein Structures Using Sparse Paramagnetic NMR Data and Physical Modeling.Frontiers in molecular biosciences · 2021Article
- Expression, epitope prediction and IgE-binding of theExperimental and therapeutic medicine · 2020Article
- Analyses of protein cores reveal fundamental differences between solution and crystal structures.Proteins · 2020Article
- Redox Systems Biology: Harnessing the Sentinels of the Cysteine Redoxome.Antioxidants & redox signaling · 2020Review
- Protein Footprinting and X-ray Crystallography Reveal the Interaction of PD-L1 and a Macrocyclic Peptide.Biochemistry · 2020Article
- Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation.Science signaling · 2020Article
- Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine.Biochimica et biophysica acta. General subjects · 2019Article
- Structural Consideration of the Working Mechanism of Fold Type I Transaminases From Eubacteria: Overt and Covert Movement.Computational and structural biotechnology journal · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR - X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution.
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.