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BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
Genís Bayarri1, Pau Andrio2, Adam Hospital1
1Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10-12, 08028 Barcelona, Spain.
Nucleic Acids Research
|May 31, 2022
Summary
BioExcel Building Blocks Workflows provides an intuitive graphical user interface for biomolecular simulation. This web-based tool simplifies common tasks like Molecular Dynamics setup and protein-ligand docking, enhancing research efficiency.
Area of Science:
- Computational Biology
- Biophysics
- Cheminformatics
Background:
- Biomolecular simulations are crucial for understanding biological processes.
- Repetitive setup and analysis tasks can be time-consuming for researchers.
- Access to user-friendly tools is essential for broader adoption of simulation methods.
Purpose of the Study:
- To introduce BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI).
- To provide easy access to pre-configured biomolecular simulation workflows.
- To streamline common and repetitive processes in biomolecular simulation research.
Main Methods:
- Development of a web-based GUI integrating the BioExcel Building Blocks library.
- Implementation of workflows for Molecular Dynamics setup, protein-ligand docking, trajectory analysis, and small molecule parameterization.
- Integration with visualization tools (NGL viewer, MDsrv) and plotting libraries (Plotly).
Main Results:
- A collection of transversal, pre-configured biomolecular simulation workflows is now accessible.
- Users can launch workflows on the platform, download them, or run them remotely on High-Performance Computers.
- The GUI offers interactive visualization of 3D structures and trajectories, and exploration of 2D plots.
Conclusions:
- BioExcel Building Blocks Workflows simplifies complex biomolecular simulation tasks.
- The tool enhances user experience through an intuitive interface and interactive features.
- It supports efficient research by automating common simulation processes and facilitating collaboration.
