Dear all, The generation of reliable restraints for novel small-molecule ligands in macromolecular complexes is of great importance for both ligand placement into density maps and subsequent refinement.
Eleven years ago we announced on the ccp4bb the availability of the Grade Web Server (GWS): https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;94bd95fa.1203 The GWS is still going strong and can be found at https://grade.globalphasing.org/ The GWS allowed users to run the Grade ligand restraint generator on any non-confidential ligand. The main source of restraint information for Grade 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 computational chemistry procedures to obtain the restraint values. As well as CIF restraints (that can be used with Coot, Refmac, BUSTER and many other programs), the GWS has the option to produce restraints for SHELX refinement. The GWS allows users to produce restraints without installing the CSD or other software. In December the GWS had a major upgrade and now runs Grade2 https://gphl.gitlab.io/grade2/. The GWS user interface has been simplified. Also included is support for a wider range of input and output file formats such as SDF. Grade2 has many improvements over Grade, such as better treatment of planar groups. In these first eleven years of service, the GWS has been used to produce restraints for over 22,000 ligands. The GWS is used by scientists from across the world so far: this year it has been used in 31 different countries. We would like to thank users for bug reports, suggestions, discussions, and feedback. We are grateful to the CCDC for their continued support of the service. With best wishes, The Global Phasing developers: Gerard Bricogne, Claus Flensburg, Peter Keller, Wlodek Paciorek, Andrew Sharff, Oliver Smart, Clemens Vonrhein, and Thomas Womack. P.S. There is now a wide range of excellent restraint generation programs available, as reviewed by Steiner and Tucker, 2017 (https://doi.org/10.1107/S2059798316017964), including CCP4 ACEDRG and Phenix eLBOW. In most cases, good results can be obtained with all of these but for unusual chemistry it is often worth trying another program. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
