Grade Web Server http://grade.globalphasing.org

Introduction

Grade generates geometrical restraints for novel small molecules. It does so by querying the Cambridge Structural Database (CSD) as a main source of restraint information, and then invoking quantum chemical procedures to obtain whatever information the CSD is unable to supply. Grade takes a SMILES string or a mol2 file containing 3D coordinates of all atoms as input. For compounds that are already in the PDB chemical components dictionary, Grade can produce restraints given the PDB 3-letter code. For novel large and complex systems the preparation and upload of a mol2 file is recommended. Please see preferred input formats help page for further information. Please note that there are limitations regarding which element types can be handled by Grade.

News:

• Maintenance: Latest versions of Grade (27 Nov 2018) installed and updated to CSD 2019. 14 December 2018
• Maintenance: updated to CSD 2018. 3 March 2018
• Maintenance: Latest versions of Grade (20 Sep 2017) installed and CSD database updated. When giving a PDB compound identifier for which no ideal coordinates are available, we now fall back to the experimental coordinates to avoid a failure for those compounds. 22 September 2017
• Maintenance: Latest versions of Grade (7th Dec 2016) and Mogul (CSD 2017) installed. 17 February 2017
• Maintenance: Latest versions of Grade and Mogul installed: details.. 29 March 2015
• Bug fixes. 20 February 2014
• Major upgrade to Grade Web Server with new features and improvements. 20 December 2013

For further details please see Grade Web Server Help Page on the BUSTER wiki.

Run Grade

Acknowledgements

Grade is developed at Global Phasing Ltd.

Big thanks to:

• CCDC for permission to use Mogul on the Grade Web Server
• Garib Murshudov and CCP4 for libcheck currently used to interpret SMILES strings
• Martin Field for the fdynamo implementation of the RM1 semiempirical QM method
• PyMOL and Open Babel
• Members of the Global Phasing Consortium and European Commission project SILVER (FP7-HEALTH-F3-2010-260644) for financial support
• BUSTER and grade users for suggestions, discussion, feedback and bug reports. Particular thanks to all the Grade web Server pre-release testers for their help!

For help and further details see Grade Web Server Help Page on the BUSTER wiki.

Please email buster-develop@globalphasing.com with any problems, queries or suggestions.

version Release v1.105 Mar 09 2018