ArticleFrontiers in molecular biosciences2020
Properties of Cavities in Biological Structures-A Survey of the Protein Data Bank.
Article in Frontiers in molecular biosciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed.
- Theoretical Methods for Assessing the Density of Protein Nanodroplets.International journal of molecular sciences · 2025Article
- Presence of EGF ligand restricts the binding ability of EgB4 nanobody to EGFR extracellular domain.Scientific reports · 2025Article
- Clustering-based Method for Constructing the Phase Diagram of the van der Waals Model Fluid.Current protein & peptide science · 2025Article
- Unbiased MD simulations identify lipid binding sites in lipid transfer proteins.The Journal of cell biology · 2024Article
- Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics.Scientific reports · 2024Article
- Redesign of γ-glutamyl transpeptidase from Bacillus subtilis for high-level production of L-theanine by cavity topology engineering.Applied microbiology and biotechnology · 2023Article
- A Structural Analysis of Proteinaceous Nanotube Cavities and Their Applications in Nanotechnology.Nanomaterials (Basel, Switzerland) · 2022Review
- Systematic analysis of membrane contact sites ineLife · 2022Article
- Nascent Folding of Proteins Across the Three Domains of Life.Frontiers in molecular biosciences · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We performed a PDB-wide survey of proteins to assess their cavity content, using the SPACEBALL algorithm to calculate the cavity volumes. In addition, we determined the hydropathy character of the cavities. We demonstrate that the cavities of most proteins are hydrophilic, but smaller proteins tend to have cavities with hydrophobic walls. We propose criteria for distinguishing between cavities and pockets, and single out proteins with the largest cavities.
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.