ArticleBioinformatics (Oxford, England)2020
atomium-a Python structure parser.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 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
10 citing papers in PubMed.
- Atomistic scattering modeling of the solution structure of human dimeric IgA1 reveals a structural and mechanistic basis for IgA nephropathy.The Journal of biological chemistry · 2026Article
- Predicting small molecule-RNA interactions without RNA tertiary structures.Nature biotechnology · 2026Article
- SBILib: a handle for protein modeling and engineering.Bioinformatics (Oxford, England) · 2023Article
- BeEM: fast and faithful conversion of mmCIF format structure files to PDB format.BMC bioinformatics · 2023Article
- Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins.Briefings in bioinformatics · 2022Article
- PDBeCIF: an open-source mmCIF/CIF parsing and processing package.BMC bioinformatics · 2021Article
- InterMetalDB: A Database and Browser of Intermolecular Metal Binding Sites in Macromolecules with Structural Information.Journal of proteome research · 2021Article
- Article
- Zincbindpredict-Prediction of Zinc Binding Sites in Proteins.Molecules (Basel, Switzerland) · 2021Article
- GraphQL for the delivery of bioinformatics web APIs and application to ZincBind.Bioinformatics advances · 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
2 authors.
Funding
Abstract
summaryStructural biology relies on specific file formats to convey information about macromolecular structures. Traditionally this has been the PDB format, but increasingly newer formats, such as PDBML, mmCIF and MMTF are being used. Here we present atomium, a modern, lightweight, Python library for parsing, manipulating and saving PDB, mmCIF and MMTF file formats. In addition, we provide a web service, pdb2json, which uses atomium to give a consistent JSON representation to the entire Protein Data Bank. AVAILABILITY AND IMPLEMENTATION: atomium is implemented in Python and its performance is equivalent to the existing library BioPython. However, it has significant advantages in features and API design. atomium is available from atomium.bioinf.org.uk and pdb2json can be accessed at pdb2json.bioinf.org.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.