NAISS
SUPR
NAISS Projects
SUPR
A pilot macromolecular 3D structure determination project - Year 15
Dnr:

NAISS 2026/3-674

Type:

NAISS Medium

Principal Investigator:

Martin Moche

Affiliation:

Karolinska Institutet

Start Date:

2026-09-01

End Date:

2027-09-01

Primary Classification:

10601: Structural Biology

Allocation

Abstract

PReSTO is a national software environment supporting structural biology research on Swedish high-performance computing (HPC) resources. The initiative began in 2013 as an outreach activity of the National Supercomputer Centre (NSC) towards Protein Science Facility (PSF) at Karolinska Institutet to evaluate macromolecular X-ray crystallography (MX) applications on the Triolith supercomputer. In 2015, MAX IV funded an expansion of PReSTO, called a MAX IV satellite, to support MX, Nuclear Magnetic Resonance (NMR), and Cryo-Electron Microscopy (Cryo-EM) workflows. Since 2017, PReSTO has been built and maintained using EasyBuild, providing a portable and version-controlled software stack with explicit dependency management. This approach enables efficient migration between computing systems and ensures long-term sustainability. The project was supported by the Swedish Research Council during 2018-2023 (grant 2018-06479). Today, PReSTO supports a broad range of structural biology applications supporting MAX IV’s fragment-screening platform (1) and provided access to software for serial crystallography and time-resolved diffraction experiments at X-ray Free Electron Laser (XFEL) facilities. In 2022, the software stack was migrated to the Berzelius cluster, extending support to complete Cryo-EM workflows. In 2025, following the establishment of the new Cryo-EM facility at the MAX IV site in Lund, the full Cryo-EM PReSTO environment was installed on the Cosmos cluster. As of July 2026, PReSTO is available on NSC Tetralith, NSC Berzelius, LUNARC Cosmos, and MAX IV computing resources. Access is provided through the National Academic Infrastructure for Supercomputing in Sweden (NAISS), with ThinLinc enabling remote graphical applications such as Coot, Chimera, CCP4mg, and PyMOL. To support users, the project maintains comprehensive documentation, workflow descriptions, batch script examples, and a dedicated launcher interface that simplifies software access and resource allocation. The primary objective of this application is to expand PReSTO beyond the current national infrastructure and establish it on the EuroHPC Arrhenius supercomputer, providing structural biology researchers with access to a harmonized software environment across both Swedish and European HPC resources. The EasyBuild-based architecture makes this deployment straightforward while maintaining reproducibility and software consistency. In addition to the Arrhenius installation, the project will continue to maintain and update software stacks across all existing platforms, ensuring support for emerging MX, Cryo-EM, NMR, serial crystallography, and future AI-enabled structure determination workflows. Planned developments include optimization for next-generation HPC architectures, improved workflow automation, and enhanced graphical access tools. By extending PReSTO to new computational infrastructures while maintaining a common user experience, the project will strengthen national and international capacity for advanced structural biology research. 1. G. M. A. Lima et al., FragMAXapp: crystallographic fragment-screening data-analysis and project-management system. Acta Crystallogr D Struct Biol 77, 799–808 (2021).