ArticlePLoS computational biology2019
BioJava 5: A community driven open-source bioinformatics library.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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
26 citing papers in PubMed.
- Incorporating Surfaced-Induced Dissociation Mass Spectrometry Data into an AlphaFold-derived deep learning network improves protein structure prediction.bioRxiv : the preprint server for biology · 2026Article
- RCSB PDB web portal RCSB.org for biotechnology research: exploration and visualization of plastic-degrading enzymes at the atomic level in 3D.Frontiers in bioengineering and biotechnology · 2026Article
- Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study.Protein science : a publication of the Protein Society · 2025Article
- Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.The Journal of chemical physics · 2024Article
- AggreProt: a web server for predicting and engineering aggregation prone regions in proteins.Nucleic acids research · 2024Article
- RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments.Bioinformatics (Oxford, England) · 2024Article
- EncoMPASS: An encyclopedia of membrane proteins analyzed by structure and symmetry.Structure (London, England : 1993) · 2024Article
- Fast and accurate protein structure search with Foldseek.Nature biotechnology · 2024Article
- FastProtein-an automated software forPeerJ · 2024Article
- OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data.Horticulture research · 2023Article
- StarPep Toolbox: an open-source software to assist chemical space analysis of bioactive peptides and their functions using complex networks.Bioinformatics (Oxford, England) · 2023Article
- RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances.Journal of molecular biology · 2023Article
- Article
- Network Science and Group Fusion Similarity-Based Searching to Explore the Chemical Space of Antiparasitic Peptides.ACS omega · 2022Article
- RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
- Exploring protein symmetry at the RCSB Protein Data Bank.Emerging topics in life sciences · 2022Article
- PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.Journal of molecular biology · 2022Review
- EpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes.Bioinformatics and biology insights · 2022Article
- RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.Protein science : a publication of the Protein Society · 2022Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
BioJava is an open-source project that provides a Java library for processing biological data. The project aims to simplify bioinformatic analyses by implementing parsers, data structures, and algorithms for common tasks in genomics, structural biology, ontologies, phylogenetics, and more. Since 2012, we have released two major versions of the library (4 and 5) that include many new features to tackle challenges with increasingly complex macromolecular structure data. BioJava requires Java 8 or higher and is freely available under the LGPL 2.1 license. The project is hosted on GitHub at https://github.com/biojava/biojava. More information and documentation can be found online on the BioJava website (http://www.biojava.org) and tutorial (https://github.com/biojava/biojava-tutorial). All inquiries should be directed to the GitHub page or the BioJava mailing list (http://lists.open-bio.org/mailman/listinfo/biojava-l).
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.