SBGrid Portals

Retiring the SBGrid Science Portals. The SBGrid Science Portal launched in 2010 PMID 21098306. Since that time we have seen advances in cloud computing and HPC accessibility (ex OSG Connect), expanded access to computational resources, dramatic CPU performance improvements and increased adoption of GPGPU computation, improvements in crystallographic methods (ex CCP4Cloud PMID 36048148, SIMBAD PMID 29968670, MrBUMP PMID 29533225 ), and a revolution in ab-initio structure prediction in utility for structural biology with the advent of tools like AlphaFold2 PMID 34265844, RosettaFold PMID 34282049, and CollabFold PMID 35637307. As such, after over 600 WSMR jobs, 500+ DEN jobs, and many millions of CPU hours, we are retiring the SBGrid Science Portals. We would like to thank the Open Science Grid for their support, both human and computational.

Wide Search Molecular Replacement

Wide Search Molecular Replacement (WSMR) performs a molecular replacement search with the application Phaser against approximately 100,000 SCOP domains. The search results are presented in the form of an LLG/TFZ graph and computations usually converge within 4-14 days. Before you submit your computations you will need to create an SBGrid portal account (request an account here) and upload your mtz file. Protein sequence files are not required. For a full description of this method please see our publication Stokes-Rees I and Sliz P, PNAS 2010. 107(50):21476-81.

Deformable Elastic Network

Deformable Elastic Network (DEN) restraints are a powerful tool for refining structures from low-resolution X-ray crystallographic data sets. Our DEN web service provides access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, a US cyberinfrastructure. Refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources, can be completed in several hours using the DEN portal. For a full description of this service please see our publication O'Donovan D et. al, Acta Cryst. D. 2012. 68:261-7.

Computations are performed using resources provided by the Open Science Grid, which is supported by the National Science Foundation and the US Department of Energy's Office of Science. Development of the portal was supported by the National Science Foundation grant 0639193.