ReviewCurrent opinion in structural biology2013
Crystallographic model validation: from diagnosis to healing.
Review in Current opinion in structural biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution.Journal of chemical theory and computation · 2020Article
- Identification and Unusual Properties of the Master Regulator FNR in the Extreme AcidophileFrontiers in microbiology · 2019Article
- Assessment of detailed conformations suggests strategies for improving cryoEM models: Helix at lower resolution, ensembles, pre-refinement fixups, and validation at multi-residue length scale.Journal of structural biology · 2018Article
- Article
- Model validation: local diagnosis, correction and when to quit.Acta crystallographica. Section D, Structural biology · 2018Article
- MolProbity: More and better reference data for improved all-atom structure validation.Protein science : a publication of the Protein Society · 2018Article
- Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions.Structure (London, England : 1993) · 2017Article
- Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin.Structure (London, England : 1993) · 2017Article
- Joint-based description of protein structure: its application to the geometric characterization of membrane proteins.Scientific reports · 2017Article
- Article
- New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.Nucleic acids research · 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
3 authors.
Funding
Abstract
Model validation has evolved from a passive final gatekeeping step to an ongoing diagnosis and healing process that enables significant improvement of accuracy. A recent phase of active development was spurred by the worldwide Protein Data Bank requiring data deposition and establishing Validation Task Force committees, by strong growth in high-quality reference data, by new speed and ease of computations, and by an upswing of interest in large molecular machines and structural ensembles. Progress includes automated correction methods, concise and user-friendly validation reports for referees and on the PDB websites, extension of error correction to RNA and error diagnosis to ligands, carbohydrates, and membrane proteins, and a good start on better methods for low resolution and for multiple conformations.
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.