Grade Web Server


Help Page

Grade Web Server Introduction

  • The generation of reliable restraints for novel small molecule ligands in protein complexes is of great importance for both ligand placement into density maps and subsequent refinement. Consequently we developed grade, a ligand restraint generator whose main source of restraint information is the Cambridge Structural Database (CSD) of small-molecule crystal structures, queried using the MOGUL program developed by the CCDC. Where small-molecule information is lacking, Grade uses quantum chemical procedures to obtain the restraint values.
  • Grade was released to academic users as part of the BUSTER package in July 2011 and has proved popular with users. However, a problem for these academic users has been that, in order to get the best restraints from Grade, a CSD system licence is necessary in order to be able to use MOGUL. Although many institutions already have CSD site licences, and otherwise licences are available at a reasonable cost, this has prevented the use of Grade by small groups and occasional users.
  • To provide easy access to Grade the CCDC has kindly agreed that we can provide a free-to-use Grade Web Server that includes the use of MOGUL in its invocation of Grade.
  • The Grade Web Server was publicly announced on 19 March 2012
  • Please note that use of the Grade Web Server is subject to agreeing to the conditions of use
  • Please do let us know about any problems you encounter or suggestions you have.

Grade Web Server Versions and Improvements

  • 11 December 2019
    • Update to latest BUSTER release, including major fixes to generation of planar restraint generation
    • Support for handling hydrogens at electron-cloud distances (as adequate for X-Ray diffraction): by default the nuclear position is assumed and used.
  • 14 December 2018
    • updated to CSD 2019
  • 3 March 2018
    • updated to CSD 2018
  • 22 September 2017 (v1.104)
    • Update to grade release 1.2.13 <August 12 2017>
    • Modified behaviour when giving a known PDB compound identifier: instead of immediately failing if no set of "ideal" coordinates could be found, now fall back onto "experimental" coordinates as a starting point.
  • 17 February 2017 (v1.103)
    • Update to Mogul 2017 release and grade release 1.2.12 <October 4 2016>
  • 29 March 2015 (v1.102)
    • Update to Mogul 2015 release and grade release 1.2.9 <July 24 2014>.
    • Detailed information about the Mogul/CSD version and QM method used is now included in the results page and output cif dictionary.
    • If the grade cif dictionary is used in BUSTER the buster-report ligands page can include hyperlinks to databases such as the PDB (see example)
    • Grade Web Server result web page now invokes google analytics to produce a world map showing where it is used from see map. This is a bit of fun. The first non-testing use was in New Zealand, next Australia followed by France and then the UK... Please note that Google is only gets information about your URL (that is then classified into a country) and web browser and NOT anything about the molecule searched for!
  • 20 February 2014 (v1.101)
    • Grade Web Server version v1.101 made live.
    • bug fix to ensure that shelx dfix files are always in included in results .tgz file.
    • bug fix to ensure that pymol pictures for compounds containing boron atoms are properly bonded
    • extension to record total charge in output .cif, .pdb and .dfix files.
  • 20 December 2013 (v1.100)
    • Grade Web Server version v1.100 released.
    • grade updated to latest pre-release (internal test version).
    • Mogul updated to use latest CSDS 2014 release.
    • New feature: output of restraints for SHELXL.
    • Many Improvements
      • Handling of phosphates.
      • Handling of groups such as biphenyls where the CSD indicates that they are not necessarily planar.
      • Set atomnames if supplied with mol2 with all atoms being named after their element type ("C", "N" etc).
      • grade_PDB_ligand will now supply dictionary with modern v3 atomnames.
      • Introduce -really_noH option for ligands that do not have any hydrogen atoms.
  • 03 April 2012 (v1.001)
    • Sorted server.cgi bug in parsing net charge (previously lost negative sign - oops!).
  • 19 March 2012 (v1.000)
    • Initial public Announcement ccp4bb message
  • 06 March 2012 (v0.004)
    • Improve charge handling in Open Babel schematic. Avoid daemon conflict by adding additional flock.
  • 04 March 2012 (v0.003)
    • recognise-compound feature added, improve SMILES handling to allow "\" and up to 300 characters
  • 22 February 2012 (v0.002)
    • start of external pre-release testing

Grade Web Server Restrictions and Limitations.

  • Please note that currently there is a limitation to which element types can be handled by grade. So currently grade does not produce dictionaries for HEM (it cannot handle Fe) or B12 (as it cannot handle Co). We intend to deal with this in the next version.
  • The molecular schematic diagram is as produced by OpenBabel. This has a tendency to get confused between neutral COOH and charged COO- groups as well as between NH2 and NH3+. Please check the pdb file and cif dictionary as this contains the actual molecule!
  • SMILES input is limited to 300 characters.
  • File uploads are currently restricted to mol2 filetype. Please see GradePreferredInputFormat for further information. We are currently working on providing better file handling.
  • Currently dictionaries are giving with old style v2.3 PDB atom naming rather than v3.0. We intend to deal with this in the next version.
  • Currently the only file type that can be uploaded is mol2 with all hydrogen atoms and unique names for each atom. We are working on accepting a much wider range of file types for the next version.
  • Currently grade is limited to use semi-empirical quantum chemical methods. We are working on extending it to be able to use ab initio and DFT QM methods that are slower but have the potential to be more accurate.
  • We need to provide pre-calculated grade results for PDB ligands - particular when slower QM procedures are involved.
  • We need to facilitate producing dictionaries for charged variants of PDB ligands.

What do Grade Web Server results pages look like?

Please address problems, corrections and clarifications to