Run Grade2 on your non-confidential ligand
Introduction
Grade2 is a tool for generating restraint dictionaries for ligands in
macromolecular structure determination.
Please see
Introduction to Grade2
,
Grade Web Server Documentation
,
and
Videos showing how to use Grade Web Server
for more information.
Latest News
- 03 July 2024
-
Grade Web Server has been updated to run the latest version of Grade2.
There are many improvements: see the Grade2
ChangeLog 1.6.0
for full details.
We have also updated to
CSD-Core version 2024.1
so that restraints are now based on over 1.25 millon CSD structures.
- 19 Jan 2024
-
The PDB is now issuing 5-character PDB Chemical Component IDs
(such as A1LU6),
having
run out of 3-character IDs.
The Grade Web Server can now produce restraints for
these cases and the input forms have been altered to stop calling the
component ID the "three-letter code".
Click to expand old news
- 25 Sep 2023
-
Support for a new option
--eh99_sigma_correction that scales up all non-hydrogen bond
and angle sigmas to match the mean sigma values of the EH99 amino
restraints used by BUSTER. For details see
an analysis comparing Grade2 and EH99 Restraints for amino acid side
chains.
- 05 July 2023
-
Grade Web Server has been updated to run the latest version of Grade2
1.4.1.
This fixes bug where Grade2 produces restraints with bond angle
sigma set to zero.
Now a minimum value of 0.3º is used for bond angle sigmas and
0.005Å for the bond sigmas.
Thanks to Christian Schleberger for reporting this bug.
See the Grade2
ChangeLog 1.4.1 for full details.
- 22 May 2023
-
Grade Web Server has been updated to run the latest version of Grade2
1.4.0.
Changes include many improvements to the 2D schematic diagrams and
CSD-based restraints for pentafluorosulfanyl SF5.
See the Grade2
ChangeLog 1.4.0 for full details.
- 14 April 2023
-
Recent problems for some PDB chemical components are now fixed
details.
Big thanks to the PDBe team, particularly Ibrahim Roshan for the fix.
- 29 December 2022
-
Added YouTube videos to the
Grade Web Server Documentation.
These aim to show a new user how to use the Grade Web Server.
Together they demonstrate producing
restraints for a ligand, including using the
PubChem Sketcher
to obtain a SMILES string starting from a molecular diagram.
- 22 December 2022
-
Update to Grade Web Server 2.0.3 <2022-12-22>
and Grade2 to 1.3.1rc1 improvements in:
- 14 December 2022
-
Major upgrade to Grade Web Server to run Grade2. Also included
is support for a wider range of input file formats such as SDF.
The user interface has been simplified.
Grade2 has many improvements over Grade, such as
better treatment of planar groups
.
Please let us know what you think of the changes.
Acknowledgements
Grade2 is developed at Global Phasing Ltd.
Many thanks to:
- CCDC for permission to use CSD
software and data on the Grade Web Server. Particular use is made of
Mogul
and the
CSD Python API .
- Developers of the excellent RDKit
chemoinformatics package used in Grade2.
- Members of the Global Phasing Consortium and European Commission project
SILVER (FP7-HEALTH-F3-2010-260644) for financial support.
- Users for bug reports, suggestions, discussion, and feedback.
Current Grade Web Server Usage Statistics
Total of 36211 successful Grade and Grade2 runs since February 2012
Click to expand
Monthly breakdown:
| Jan | Feb | Mar | Apr | May | Jun | Jul | Aug | Sep | Oct | Nov | Dec | Σ |
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 | 193 | 130 | 148 | 221 | 131 | 195 | 202 | 281 | 200 | 2316 |
2021 | 198 | 261 | 219 | 203 | 171 | 210 | 201 | 123 | 151 | 188 | 244 | 283 | 2452 |
2022 | 227 | 234 | 225 | 235 | 213 | 189 | 219 | 188 | 195 | 255 | 245 | 370 | 2795 |
2023 | 388 | 593 | 650 | 481 | 562 | 549 | 592 | 612 | 556 | 489 | 577 | 507 | 6556 |
2024 | 852 | 718 | 640 | 707 | 653 | 560 | 720 | 445 | 2693 | 977 | | | 8965 |
Run Original Grade (Deprecated)
Click to expand
If you want to run the original Grade program (rather than Grade2) this is currently still possible using the
Run Original Grade (Deprecated) interface.
Please email buster-develop@GlobalPhasing.com with any problems, queries or suggestions.
GWS version: 2.0.11 <2024-07-03>