ArticleProtein science : a publication of the Protein Society2020
New tools in MolProbity validation: CaBLAM for CryoEM backbone, UnDowser to rethink "waters," and NGL Viewer to recapture online 3D graphics.
Article in Protein science : a publication of the Protein Society, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
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Who cites it
105 citing papers in PubMed.
- The protein-water H-bond network for bacterial response regulator REC domain activation.Journal of structural biology: X · 2026Article
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- Monovalent cations differentially regulate the activity of eukaryotic fluoride channels and impact fluoride resistance.PLoS biology · 2026Article
- Predicting water at the protein interface in cryo-EM structures from MD-excess chemical potential.Biophysical journal · 2026Article
- Pan-Ebolavirus nanoparticle vaccine provides protection in rodents from lethal infection by Zaire and Sudan viruses.Nature communications · 2026Article
- Distinct Filament Conformation for Receptor-Bound Amyloid-β from Alzheimer's Disease Brain.Nature communications · 2026Article
- Structural basis for transport and inhibition of nucleotide sugar transport in pathogenic fungi.Nature communications · 2026Article
- Structural basis for prostaglandin and drug transport via SLCO2A1.Nature communications · 2026Article
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- Ancestral neuronal receptors are bacterial accessory toxins.Nature communications · 2026Article
- The molecular mechanism of fluoride export by the eukaryotic fluoride channel FEX.Nature communications · 2025Article
- Distinct Filament Conformation for Receptor-Bound Amyloid-ß from Alzheimer's Disease Brain.bioRxiv : the preprint server for biology · 2025Article
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- Categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures: near-predictive, pseudostructure and barbed wire.Acta crystallographica. Section D, Structural biology · 2025Article
- Ten rules for a structural bioinformatic analysis.PLoS computational biology · 2025Article
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- Distance-AF improves predicted protein structure models by AlphaFold2 with user-specified distance constraints.Communications biology · 2025Article
- RhoA allosterically activates phospholipase Cε via its EF hands.Communications biology · 2025Article
- gapTrick-structural characterization of protein-protein interactions using AlphaFold.Bioinformatics (Oxford, England) · 2025Article
- Structural basis for the recognition and ubiquitylation of type-2 N-degron substrate by PRT1 plant N-recognin.Nature communications · 2025Article
45 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
The MolProbity web service provides macromolecular model validation to help correct local errors, for the structural biology community worldwide. Here we highlight new validation features, and also describe how we are fighting back against outside developments which compromise that mission. Our new tool called UnDowser analyzes the properties and context of clashing HOH "waters" to diagnose what they might actually represent; a dozen distinct scenarios are illustrated and described. We now treat alternate conformations more thoroughly, and switching to the Neo4j database (graphical rather than relational) enables cleaner, more comprehensive, and much larger reference datasets. A problematic outside change is that refinement software now increasingly restrains traditional validation criteria (geometry, clashes, rotamers, and even Ramachandran) in order to supplement the sparser experimental data at 3-4 Å resolutions typical of modern cryoEM. But unfortunately the broad density allows model optimization without fixing underlying problems, which means these structures often score much better on validation than they really are. CaBLAM, our tool designed for evaluating peptide orientations at lower resolutions, was described in the previous Tools issue, and here we demonstrate its effectiveness in diagnosing local errors even when other validation outliers have been artificially removed. Sophisticated hacking of the MolProbity server has required continual monitoring and various security measures short of restricting user access. The deprecation of Java applets now prevents KiNG interactive online display of outliers on the 3D model during a MolProbity run, but that important functionality has now been recaptured with a modified version of the Javascript NGL Viewer.
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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.