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

Genís Bayarri,Modesto Orozco,Adam Hospital

doi:10.3389/fmolb.2021.726232

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.

Highlights

Since Max Perutz and colleagues solved the first 3D structure of Hemoglobin using X-ray crystallography in 1960 (Perutz et al, 1960), macromolecular structure 3D representations have become classic elements in biomolecular scientific journals and scientific discussions
Dynamics (MD) simulations (Hospital et al, 2015), Virtual Screening (VS) techniques (Walters and Wang, 2020) or protein structure predictions (Senior et al, 2020; Zhu et al, 2021) generates the need to deal in an efficient way with structures (3D) and structural ensembles (4D models, with time as a 4th dimension)
Current network bandwidths allow streaming of heavy videos at home, Central and Graphics Processing Units (CPUs, GPUs) are powerful enough to work with extremely demanding tasks, even in portable and small devices, and graphic software has improved dramatically their performance for realistic representations of the structural models

Summary

INTRODUCTION

Since Max Perutz and colleagues solved the first 3D structure of Hemoglobin using X-ray crystallography in 1960 (Perutz et al, 1960), macromolecular structure 3D representations have become classic elements in biomolecular scientific journals and scientific discussions. Current network bandwidths allow streaming of heavy videos at home, Central and Graphics Processing Units (CPUs, GPUs) are powerful enough to work with extremely demanding tasks, even in portable and small devices, and graphic software has improved dramatically their performance for realistic representations of the structural models Some of these technologies (such as WebGL) have been already used for the representation of 3D structures in a common web browser (Rego and Koes, 2015; Bekker et al, 2016; Sehnal et al, 2017; Shi et al, 2017; Perkel, 2018; Rose et al, 2018; Hildebrand et al, 2019; Sehnal et al, 2021) using native support for GPU acceleration. The 3dRS server has a very intuitive use, no registration is required and is freely available at https://mmb.irbbarcelona.org/3dRS

METHODS

RESULTS

DISCUSSION

DATA AVAILABILITY STATEMENT