Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem.

Rodrigo V Honorato,Antonio Rosato,Andrea Giachetti,Marco Verlato,Alexandre M J J Bonvin,Brian Jiménez-García,Panagiotis I Koukos,Andrei Tsaregorodtsev

doi:10.3389/fmolb.2021.729513

Abstract

Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (www.wenmr.eu) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the high throughput computing infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects and are now operating as Thematic Services in the European Open Science Cloud portal (www.eosc-portal.eu), sending >12 millions of jobs and using around 4,000 CPU-years per year. Here we review 10 years of successful e-infrastructure solutions serving a large worldwide community of over 23,000 users to date, providing them with user-friendly, web-based solutions that run complex workflows in structural biology. The current set of active WeNMR portals are described, together with the complex backend machinery that allows distributed computing resources to be harvested efficiently.

Highlights

Proteins and nucleic acids are the main biological macromolecules responsible for function and maintenance of most of the machinery of life. The study of these macromolecules, their threedimensional (3D) structure, dynamical behavior and interactions are crucial to gain a better understanding of relevant biological processes both related to biotechnological applications as well as health related such as the development of new drugs
In the context of WeNMR operating as a Thematic service provider in the European Open Science Cloud (EOSC), we have provided the community with relevant and specialized software that make up a valuable toolkit for structural biology researchers
We present an overview of the structural biology services provided via the WeNMR-EOSC ecosystem, what are the technological challenges and solutions that need to be implemented for an efficient use of distributed computing resources and how those are used by an active community worldwide

Summary

INTRODUCTION

Proteins and nucleic acids are the main biological macromolecules responsible for function and maintenance of most of the machinery of life. Powerfit has been developed as a Python package for fast and sensitive rigid body fitting of molecular structures into EM density maps with a core-weighted local cross correlation scoring function (Zundert and Bonvin, 2015b) It is freely available as a webserver (Zundert et al, 2017) running on both local and GPU-accelerated distributed infrastructures at https://alcazar.science.uu.nl/services/ POWERFIT. The project is providing a development framework and a set of ready-to-use components to build distributed computing systems of arbitrary complexity It provides a complete solution for communities needing access to computing and storage resources distributed geographically, integrated in different grid and cloud infrastructures or standalone computing clusters and supercomputers. During the COVID pandemic, one of the most used WeNMR service, HADDOCK, has seen a significant increase of both the number of submissions and single users, with about 1/3 of all submissions since April 2021 being COVID-related (Figure 3)

CONCLUSION

DATA AVAILABILITY STATEMENT