BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations

TitleBioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
Publication TypeJournal Article
Year of Publication2022
AuthorsBayarri, Genis, Andrio Pau, Hospital Adam, Orozco Modesto, and Gelpí Josep Lluís
JournalNucleic Acids Res
VolumeIn Press
Paginationgkac380
Date Published05/2022
ISBN Number0305-1048
Abstract

We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library. Available workflows include Molecular Dynamics setup, protein-ligand docking, trajectory analyses and small molecule parameterization. Workflows can be launched in the platform or downloaded to be run in the users’ own premises. Remote launching of long executions to user's available High-Performance computers is possible, only requiring configuration of the appropriate access credentials. The web-based graphical user interface offers a high level of interactivity, with integration with the NGL viewer to visualize and check 3D structures, MDsrv to visualize trajectories, and Plotly to explore 2D plots. The server requires no login but is recommended to store the users’ projects and manage sensitive information such as remote credentials. Private projects can be made public and shared with colleagues with a simple URL. The tool will help biomolecular simulation users with the most common and repetitive processes by means of a very intuitive and interactive graphical user interface. The server is accessible at https://mmb.irbbarcelona.org/biobb-wfs.

URLhttps://doi.org/10.1093/nar/gkac380
Short TitleNucleic Acids Research
Highlight: 
Review: