Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

doi:10.3389/fmolb.2021.729513

. 2021 Jul 28:8:729513.

doi: 10.3389/fmolb.2021.729513. eCollection 2021.

Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

Rodrigo V Honorato¹, Panagiotis I Koukos¹, Brian Jiménez-García¹, Andrei Tsaregorodtsev², Marco Verlato³, Andrea Giachetti⁴, Antonio Rosato⁴, Alexandre M J J Bonvin¹

Affiliations

¹ Bijvoet Centre for Biomolecular Research, Faculty of Science, Department of Chemistry, Utrecht University, Utrecht, Netherlands.
² Aix Marseille University, CNRS/IN2P3, CPPM, Marseille, France.
³ INFN, Sezione di Padova, Padova, Italy.
⁴ Department of Chemistry and Magnetic Resonance Center, University of Florence, and C.I.R.M.M.P, Fiorentino, Italy.

PMID: 34395534
PMCID: PMC8356364
DOI: 10.3389/fmolb.2021.729513

Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

Rodrigo V Honorato et al. Front Mol Biosci. 2021.

. 2021 Jul 28:8:729513.

doi: 10.3389/fmolb.2021.729513. eCollection 2021.

Authors

Rodrigo V Honorato¹, Panagiotis I Koukos¹, Brian Jiménez-García¹, Andrei Tsaregorodtsev², Marco Verlato³, Andrea Giachetti⁴, Antonio Rosato⁴, Alexandre M J J Bonvin¹

Affiliations

¹ Bijvoet Centre for Biomolecular Research, Faculty of Science, Department of Chemistry, Utrecht University, Utrecht, Netherlands.
² Aix Marseille University, CNRS/IN2P3, CPPM, Marseille, France.
³ INFN, Sezione di Padova, Padova, Italy.
⁴ Department of Chemistry and Magnetic Resonance Center, University of Florence, and C.I.R.M.M.P, Fiorentino, Italy.

PMID: 34395534
PMCID: PMC8356364
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.

Keywords: distributed computing; e-infrastructure; structural biology; web portal; web services.

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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. BJ-G is the editor of the “Web Tools for Modeling and Analysis of Biomolecular Interactions” research topic.

Figures

**FIGURE 1**
Schematic panel displaying which type of input data and restraint are supported by each WeNMR-EOSC service as well as execution infrastructure used, registration policy and certificate handling.

**FIGURE 2**
Usage of EOSC/EGI HTC resources per year in terms of normalized CPU hours for the WeNMR services (source EGI accounting portal).

**FIGURE 3**
Number of submissions **(A)** and unique active users **(B)** per month of the HADDOCK WeNMR portal since 2019. An active user is a user who has submitted at least one run to the portal during the specified period. Since April 2020 users can flag their submission as COVID-related (orange bars). Those represent about 1/3 of the total number of submissions.

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[1] Ambrosetti F., Olsen T. H., Olimpieri P. P., Jiménez-García B., Milanetti E., Marcatilli P., et al. (2020). proABC-2: PRediction of AntiBody Contacts V2 and its Application to Information-Driven Docking. Bioinformatics 36, 5107–5108. 10.1093/bioinformatics/btaa644 - DOI - PMC - PubMed

[2] Ambrosetti F., Olsen T. H., Olimpieri P. P., Jiménez-García B., Milanetti E., Marcatilli P., et al. (2020). proABC-2: PRediction of AntiBody Contacts V2 and its Application to Information-Driven Docking. Bioinformatics 36, 5107–5108. 10.1093/bioinformatics/btaa644 - DOI - PMC - PubMed

[3] Andreetto P., Astalos J., Dobrucky M., Giachetti A., Rebatto D., Rosato A., et al. (2017). EGI Federated Platforms Supporting Accelerated Computing. Proc. Int. Symp. Grids Clouds Isgc 2017, Pos Isgc2017. 10.22323/1.293.0020 - DOI

[4] Andreetto P., Astalos J., Dobrucky M., Giachetti A., Rebatto D., Rosato A., et al. (2017). EGI Federated Platforms Supporting Accelerated Computing. Proc. Int. Symp. Grids Clouds Isgc 2017, Pos Isgc2017. 10.22323/1.293.0020 - DOI

[5] Andreini C., Cavallaro G., Lorenzini S., Rosato A. (2013a). MetalPDB: a Database of Metal Sites in Biological Macromolecular Structures. Nucleic Acids Res. 41, D312–D319. 10.1093/nar/gks1063 - DOI - PMC - PubMed

[6] Andreini C., Cavallaro G., Lorenzini S., Rosato A. (2013a). MetalPDB: a Database of Metal Sites in Biological Macromolecular Structures. Nucleic Acids Res. 41, D312–D319. 10.1093/nar/gks1063 - DOI - PMC - PubMed

[7] Andreini C., Cavallaro G., Rosato A., Valasatava Y. (2013b). MetalS2: A Tool for the Structural Alignment of Minimal Functional Sites in Metal-Binding Proteins and Nucleic Acids. J. Chem. Inf. Model. 53, 3064–3075. 10.1021/ci400459w - DOI - PubMed

[8] Andreini C., Cavallaro G., Rosato A., Valasatava Y. (2013b). MetalS2: A Tool for the Structural Alignment of Minimal Functional Sites in Metal-Binding Proteins and Nucleic Acids. J. Chem. Inf. Model. 53, 3064–3075. 10.1021/ci400459w - DOI - PubMed

[9] Berman H., Henrick K., Nakamura H. (2003). Announcing the Worldwide Protein Data Bank. Nat. Struct. Mol. Biol. 10, 980. 10.1038/nsb1203-980 - DOI - PubMed

[10] Berman H., Henrick K., Nakamura H. (2003). Announcing the Worldwide Protein Data Bank. Nat. Struct. Mol. Biol. 10, 980. 10.1038/nsb1203-980 - DOI - PubMed

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Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

Affiliations

Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

Authors

Affiliations

Abstract

Conflict of interest statement

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