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. 2022 Jul 5;50(W1):W99-W107.
doi: 10.1093/nar/gkac380.

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

Genís Bayarri  1 , Pau Andrio  2 , Adam Hospital  1 , Modesto Orozco  1   3 , Josep Lluís Gelpí  2   3
Affiliations

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

Genís Bayarri et al. Nucleic Acids Res. .

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.

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Figures

Graphical Abstract
Graphical Abstract
BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows.
Figure 1.
Figure 1.
BioBB-Wfs Internal schema. The server is divided into two main blocks: front-end (left) and back-end (right).
Figure 2.
Figure 2.
BioBB-Wfs user's workspace. (A) List of projects; (B) user profile; (C) my projects instant access.
Figure 3.
Figure 3.
BioBB-Wfs project creation. Example of intermediate step: macromolecule structure checking.
Figure 4.
Figure 4.
Workflow results examples. (A) Protein–ligand docking outputs: best ligand poses; docking experiments were done with Autodock Vina. (B) Protein MD analysis: RMSd values against first and average structure. An associated NGL viewer presents the results in 3D representation.
See this image and copyright information in PMC

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