ArticleProtein science : a publication of the Protein Society2009
RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation.
Article in Protein science : a publication of the Protein Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 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
90 citing papers in PubMed.
- Structural ontogeny of protein-protein interactions.Science (New York, N.Y.) · 2026Article
- A Complementarity-Based Approach to De Novo Binder Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Predicting protein stability changes upon mutations with dual-view ensemble learning from single sequence.Briefings in bioinformatics · 2025Article
- De novo design of ATPase based on a blueprint optimized for harboring the P-loop motif.Protein science : a publication of the Protein Society · 2025Article
- Orientation-dependent CD45 inhibition with viral and engineered ligands.Science immunology · 2024Article
- Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design.Protein science : a publication of the Protein Society · 2024Article
- De novo-designed transmembrane proteins bind and regulate a cytokine receptor.Nature chemical biology · 2024Article
- Systematic computer-aided disulfide design as a general strategy to stabilize prefusion class I fusion proteins.Frontiers in immunology · 2024Article
- The design of functional proteins using tensorized energy calculations.Cell reports methods · 2023Article
- Exploration of novel αβ-protein folds through de novo design.Nature structural & molecular biology · 2023Article
- Deploying synthetic coevolution and machine learning to engineer protein-protein interactions.Science (New York, N.Y.) · 2023Article
- De novo designed ice-binding proteins from twist-constrained helices.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection.International journal of molecular sciences · 2023Article
- Article
- Core packing of well-defined X-ray and NMR structures is the same.Protein science : a publication of the Protein Society · 2022Article
- Tertiary motifs as building blocks for the design of protein-binding peptides.Protein science : a publication of the Protein Society · 2022Article
- A topological refactoring design strategy yields highly stable granulopoietic proteins.Nature communications · 2022Article
- Protein sequence design with a learned potential.Nature communications · 2022Article
- De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design.Biodesign research · 2022Article
- Tunable Heteroassembly of a Plant Pseudoenzyme-Enzyme Complex.ACS chemical biology · 2021Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
We present a novel method called RosettaHoles for visual and quantitative assessment of underpacking in the protein core. RosettaHoles generates a set of spherical cavity balls that fill the empty volume between atoms in the protein interior. For visualization, the cavity balls are aggregated into contiguous overlapping clusters and small cavities are discarded, leaving an uncluttered representation of the unfilled regions of space in a structure. For quantitative analysis, the cavity ball data are used to estimate the probability of observing a given cavity in a high-resolution crystal structure. RosettaHoles provides excellent discrimination between real and computationally generated structures, is predictive of incorrect regions in models, identifies problematic structures in the Protein Data Bank, and promises to be a useful validation tool for newly solved experimental structures.
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.