A pilot macromolecular 3D structure determination project - Year 7
||A pilot macromolecular 3D structure determination project - Year 7|
||SNIC Medium Compute|
||Martin Moche <Martin.Moche@ki.se>|
||2019-06-03 – 2020-07-01|
||10203 10601 |
In March 2013 Protein Science Facility (PSF) from Karolinska Institutet in Stockholm and National Supercomputer Centre (NSC) in Linköping started a pilot project to evaluate Macromolecular X-ray crystallography (MX) applications performance at NSC Triolith. In 2015, the Swedish light source MAX IV decided to fund a pilot extension called PReSTO(https://www.nsc.liu.se/support/presto/), that aim to support integrated structural biology calculations including MX, Nuclear Magnetic Resonance (NMR) and cryo-electron microscopy (cryo-EM).
Access to the PReSTO installation is via Swedish National Infrastructure of Computing (SNIC) funded by the Swedish research council (www.snic.vr.se). Thinlinc software from cendio https://www.cendio.com/thinlinc/what-is-thinlinc supports the integrated structural biology workflow by enabling remote graphic applications such as coot/chimera/ccp4mg/pymol for model building, calculation and visualization of protein structure and surface properties.
The PReSTO homepage (https://www.nsc.liu.se/support/presto/) intended for HPC-MX newcomers pointing towards MX software developer manuals. To adapt new users to the MX-HPC workflow we also developed a PReSTO menu that A) launch MX software at login or compute node with graphics support B) enable user to select number of cores and runtime at compute nodes C) enable user to select output directory for software such as hkl2map.
During 2017-2018 the PReSTO HPC-MX installation was made using easybuild (https://easybuild.readthedocs.io/en/latest/) with several advantages to a standard HPC installation such as A) software environments can be send to compute nodes B) software dependencies are visible in easyconfigs. PReSTO for MX is now available at NSC Triolith, LUNARC Aurora and the MAX IV cluster. During 2019, the PReSTO installation will be placed under version control.
In September 2019, we want to share easybuild daily maintenance/operations with local HPC administrators at the MAX IV site. Swedish researchers visiting BioMAX recieve some MX-HPC training during beamtime. Regular after beamtime training sessions with users own data/questions will be available at drop-in sessions at protein science facility, Karolinska Institutet. Startup PReSTO seminar/workshop can also be requested by all Swedish Universities by contacting project PI (Martin Moche) as done by UU in 2015 and SLU in 2018.
Please acknowledge SNIC (https://www.snic.se/allocations/apply4access/) when using its resources (1-3)
1. M. Anandapadamanaban et al., Mutation-Induced Population Shift in the MexR Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for MarR Family Derepression. Structure 24, 1311-1321 (2016).
2. A. Janfalk Carlsson et al., Laboratory-Evolved Enzymes Provide Snapshots of the Development of Enantioconvergence in Enzyme-Catalyzed Epoxide Hydrolysis. Chembiochem, (2016).
3. J. S. Brock et al., A dynamic Asp-Arg interaction is essential for catalysis in microsomal prostaglandin E2 synthase. Proceedings of the National Academy of Sciences of the United States of America 113, 972-977 (2016).