Grade Web Server

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

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 help , Grade Web Server Documentation help , and Videos showing how to use Grade Web Server help for more information.

Latest News

25 September 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:

Fixed bug where Grade2 terminates with IndexError: string index out of range for large ligands that have more than 26 five-membered or six-membered rings. Thanks to Deepak Deepak for reporting this bug. (#532)

Fixed bug where Grade2 produced SHELXL restraint files with REM comment lines longer than 80 characters that SHELX cannot process. Thanks to Tim Gruene for reporting this bug. (#544)
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 25705 successful Grade and Grade2 runs since February 2012

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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 32 5015

	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	32			5015

Run Original Grade (Deprecated)

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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: 2.0.9 <2023-09-25>