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. 2021 Aug 13:8:726232.
doi: 10.3389/fmolb.2021.726232. eCollection 2021.

3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories

Genís Bayarri  1 , Adam Hospital  1 , Modesto Orozco  1   2
Affiliations

3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories

Genís Bayarri et al. Front Mol Biosci. .

Abstract

3D Representation Sharing (3dRS) is a web-based tool designed to share biomolecular structure representations, including 4D ensembles derived from Molecular Dynamics (MD) trajectories. The server offers a team working in different locations a single URL to share and discuss structural data in an interactive fashion, with the possibility to use it as a live figure for scientific papers. The web tool allows an easy upload of structures and trajectories in different formats. The 3D representation, powered by NGL viewer, offers an interactive display with smooth visualization in modern web browsers. Multiple structures can be loaded and superposed in the same scene. 1D sequences from the loaded structures are presented and linked to the 3D representation. Multiple, pre-defined 3D molecular representations are available. The powerful NGL selection syntax allows the definition of molecular regions that can be then displayed using different representations. Important descriptors such as distances or interactions can be easily added into the representation. Trajectory frames can be explored using a common video player control panel. Trajectories are efficiently stored and transferred to the NGL viewer thanks to an MDsrv-based data streaming. The server design offers all functionalities in one single web page, with a curated user experience, involving a minimum learning curve. Extended documentation is available, including a gallery with a collection of scenes. The server requires no registration and is available at https://mmb.irbbarcelona.org/3dRS.

Keywords: 3D representation; FAIR; biomolecular structures; data sharing; interactive figures; molecular dynamics.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
3D Representation Sharing infrastructure scheme, composed of two main sections: the front-end, powered by a combination of VueJS, HTML5 and CSS3; and the back-end, powered by a combination of PHP-Slim REST API, MDsrv MD trajectory streaming server, and mongoDB NoSQL database. The back-end tools are implemented in Virtual Machines (VM) deployed in an OpenNebula cloud infrastructure.
FIGURE 2
FIGURE 2
3dRS Edition Mode panels. (A) Stage panel; (B) Tools; (C) Representations; (D) Selections; (E) Sharing; (F) 1D Sequence.
FIGURE 3
FIGURE 3
3dRS Shared Mode panels. (A) Stage panel; (B) Tools; (C) Caption; (D) Forking; (E) Player.
FIGURE 4
FIGURE 4
SARS-CoV-2 example. (A) Spike trimeric protein; https://mmb.irbbarcelona.org/3dRS/s/c1tOez; (B) Spike with one RDB domain in “up” position; https://mmb.irbbarcelona.org/3dRS/s/hfS2rW; (C) Spike (monomer) with P5A-1B9 Fab antibody attached to the RBD domain; https://mmb.irbbarcelona.org/3dRS/s/lQ6f21; (D) Spike (monomer) with 1–87 antibody attached to the NTD domain; https://mmb.irbbarcelona.org/3dRS/s/hJxjZv (E) Insight of RBD-Antibody interface; https://mmb.irbbarcelona.org/3dRS/s/JcshuF (F) Insight of NTD-Antibody interface; https://mmb.irbbarcelona.org/3dRS/s/YiGhxv.
FIGURE 5
FIGURE 5
SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp) study. (A) Interactive representation of RdRp bound to its essential co-factors nsp7 and nsp8; https://mmb.irbbarcelona.org/3dRS/s/7Rn2Ka; (B) Exploring the ability of RdRp to incorporate a natural triphosphate into a nascent RNA; https://mmb.irbbarcelona.org/3dRS/s/TKf8yA.
FIGURE 6
FIGURE 6
Collective variables example. (A) D-Ribose binding protein; https://mmb.irbbarcelona.org/3dRS/s/nDM5sO; (B) Calcium Saturated Cardiac Troponin C; https://mmb.irbbarcelona.org/3dRS/s/QGAgYO.
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