ArticleScientific data2019
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows.
Article in Scientific data, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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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.
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Who cites it
21 citing papers in PubMed.
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
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- TMEM63 proteins act as mechanically activated cholesterol modulated lipid scramblases contributing to membrane mechano-resilience.Nature communications · 2026Article
- Computational Analysis of a Next-Generation Platinum-Based Chemotherapies that Induce DNA Double-Strand Breaks.Journal of chemical information and modeling · 2026Article
- A Machine Learning Model for the Proteome-Wide Prediction of Lipid-Interacting Proteins.Journal of chemical information and modeling · 2025Article
- CGeNArateWeb: a web server for the atomistic study of the structure and dynamics of chromatin fibers.Nucleic acids research · 2025Article
- Overcoming Clusterin-Induced Chemoresistance in Cancer: A Computational Study Using a Fragment-Based Drug Discovery Approach.Biology · 2025Article
- In Vitro and In Silico Studies on the Anti-H1N1 Activity of Bioactive Compounds from Marine-DerivedMarine drugs · 2025Article
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- Comprehensive detection and characterization of human druggable pockets through binding site descriptors.Nature communications · 2024Article
- Developments and applications of the OPTIMADE API for materials discovery, design, and data exchange.Digital discovery · 2024Article
- Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows.PLoS computational biology · 2024Article
- Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.Biophysical journal · 2023Article
- Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs.bioRxiv : the preprint server for biology · 2023Article
- Conserved Water Networks Identification for Drug Design Using Density Clustering Approaches on Positional and Orientational Data.Journal of chemical information and modeling · 2022Article
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
- pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science.BMC bioinformatics · 2021Article
- Intelligent Building Construction Management Based on BIM Digital Twin.Computational intelligence and neuroscience · 2021Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the "bioinformatics way of working". The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB's are built as Python wrappers to provide an interoperable architecture. BioBB's have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.
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.