Grade Web Server

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:

Upgrade to Grade (29 Nov 2019, including multiple improvements and bug fixes), added electron-cloud option and updated CSD database. 11 December 2019 '
Please note that the option to generate dictionaries without the use of the CSD has been removed.
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!

Current usage statistics (updated every 10 min):

 YEAR   Jan   Feb   Mar   Apr   May   Jun   Jul   Aug   Sep   Oct   Nov   Dec  TOTAL
 -----------------------------------------------------------------------------------
 2012           7    70    79   105    81    84    43    33   139    73    51    765
 2013    91    54    70    53    63    38    69    31    39    61    85    58    712
 2014    49   154    48    63    74    83   133   146    91   147    59    92   1139
 2015    79   121    73   142   144   122   132   120    95   111    78    83   1300
 2016   163   165   106   129   229   118   232   170   139   157   107   134   1849
 2017   122   169   168   126   166   201   292   169   159   213   165   128   2078
 2018   169   205   248   214   227   323   492   179   185   231   203   208   2884
 2019   159   155   349   226   272   150   253   104   162   225   163   182   2400
 2020   165   235   215    77                                                    692

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 v1.106 Dec 11 2019