ArticleNucleic acids research2015
A series of PDB-related databanks for everyday needs.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 452 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
452 citing papers in PubMed.
- Structural and functional consequences of IL33 and IL1RL1 coding variants on IL-33/ST2 signaling.Genes and immunity · 2026Article
- AI-enabled discovery and biochemical optimization of minibinders targeting cancer cell-surface proteins.Nature communications · 2026Article
- Variant characterization in the intrinsically disordered human proteome.Nature structural & molecular biology · 2026Article
- Comparing Enhanced Sampling Methods in Exploring the Conformational Space of β-CateninThe journal of physical chemistry. B · 2026Article
- Temperature-Dependent Menthol Binding across TRPM8 Conformational States.Journal of the American Chemical Society · 2026Article
- SGGly: a web server for whole-protein, structure-guided analysis of candidate N-linked glycosylation sites.Nucleic acids research · 2026Article
- BAM-BepA complexes in outer membrane protein quality control.Nature communications · 2026Article
- Doxorubicin-driven reconfiguration of BSA-cushioned DPPC liposomes an integrated molecular-dynamics and AFM roadmap for next-generation drug-delivery platforms.Nanoscale advances · 2026Article
- BiMba: using Vision Mamba to predict protein sites that bind other proteins.Bioinformatics (Oxford, England) · 2026Article
- Ovo, an open-source ecosystem for de novo protein design.Communications biology · 2026Article
- Integrative Structural Bioinformatics and Molecular Dynamics Analyses of Synaptic Vesicle Proteins and Their Water-Soluble QTY-Variants Reveal Membrane Constraints and Evolutionary Coupling of T ⇔ V.Journal of molecular evolution · 2026Article
- Programmable DNA Folding Modulates Phase Behavior and Dynamics of DNA/Peptide Condensates.ACS nano · 2026Article
- MuFGPS: enhancing liquid-liquid phase separation protein prediction through multi-level features and ensemble learning.Briefings in bioinformatics · 2026Article
- Cytoplasmic abundant heat-soluble proteins from tardigrades protect synthetic cells under stress.Nature communications · 2026Article
- Plant-associated fungi co-opt ancient antimicrobials for host manipulation.Science advances · 2026Article
- Anxiolytic-like effects of p-coumaric acid via GABAergic interaction pathways: an in vivo and in silico study.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- SegDesign: A modular framework for controllable protein segment engineering.Protein science : a publication of the Protein Society · 2026Article
- DEX: a consensus-based amino acid exchangeability measure for improved codon substitution modelling.bioRxiv : the preprint server for biology · 2026Article
- Article
- Protein structure and selection pressure in plants: using mutation to understand the functional importance of protein structure.BMC genomics · 2026Article
392 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
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a series of databanks (http://swift.cmbi.ru.nl/gv/facilities/) that hold information that is computationally derived from Protein Data Bank (PDB) entries and that might augment macromolecular structure studies. These derived databanks run parallel to the PDB, i.e. they have one entry per PDB entry. Several of the well-established databanks such as HSSP, PDBREPORT and PDB_REDO have been updated and/or improved. The software that creates the DSSP databank, for example, has been rewritten to better cope with π-helices. A large number of databanks have been added to aid computational structural biology; some examples are lists of residues that make crystal contacts, lists of contacting residues using a series of contact definitions or lists of residue accessibilities. PDB files are not the optimal presentation of the underlying data for many studies. We therefore made a series of databanks that hold PDB files in an easier to use or more consistent representation. The BDB databank holds X-ray PDB files with consistently represented B-factors. We also added several visualization tools to aid the users of our databanks.
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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.