You can download a database of protein ligands (extracted from their PDB files, and fragmented) for SHOP here:

PDBBIND

It is compressed using tar and gzip. To extract it, copy the file "pdbbind.tar.gz" inside SHOP_INSTALLDIR/databases/ folder and then write: tar -zxvf pdbbind.tar.gz

Once it has finished extracting the files, you must remove the pdbbind.tar.gz (or save it elsewhere) from "databases" folder, as Shop server expects to find only databases there.

It contains:
Number of scaffolds with 1 anchor point = 7452

This Shop database was created out of the published scaffolds of the Journal of Combinatorial Chemistry (1999 up to 2005):

Click on CombChemDB to download this Shop database.

Users of this database should be aware that it's a rather small database , and has not been updated since 2005.

It contains:
Number of scaffolds with 1 anchor point = 3089
Number of scaffolds with 2 anchor points = 4064
Number of scaffolds with 3 anchor points = 2824
Number of scaffolds with 4 anchor points = 873
Number of scaffolds with 5 anchor points = 188
Total Number of Scaffolds = 11038

REFERENCES

1. 
   Bergmann R, Linusson A, Zamora I.
   SHOP: Scaffold HOPping by GRID-Based Similarity Searches.

   J. Med Chem. 50(11), 2708-2717 (2007)

2. 
   Comprehensive survey of combinatorial library synthesis: 2004
   Roland E. Dolle
   J. Comb. Chem. 7, 739-798 (2005)
3. 
   Comprehensive survey of combinatorial library synthesis: 2003
   Roland E. Dolle
   J. Comb. Chem. 6, 623-679 (2004)
4. 
   Comprehensive survey of combinatorial library synthesis: 2002

   Roland E. Dolle
   J. Comb. Chem. 5, 693-753 (2003)

5. 
   Comprehensive survey of combinatorial library synthesis: 2001
   Roland E. Dolle

   J. Comb. Chem. 4, 369-418 (2002)

6. 
   Comprehensive survey of combinatorial library synthesis: 2000
   Roland E. Dolle
   J. Comb. Chem. 3, 477-517 (2001)
7. 
   Comprehensive survey of combinatorial library synthesis: 1999
   Roland E. Dolle
   J. Comb. Chem. 2, 383-433 (2000)

We have developed a second Shop Database based on a set of chemical groups

Since the number of compounds is not so large you can download the database already done

We recommend to the user to split the database computation in 4 runs that can be done in parallel. In order to do this:

1. Download the file
2. Un pack and Un Compress
3. Copy the directory in the Shop database folder

By doing this procedure you will obtain a database with 1124 structures

We have developed a second Shop Database based on the heterocyle structures as in the Heterocycle 01 case. In this second database we have used all the reactions in the Reaction_01.rxn and only two rounds of Virtual reaction.

Since the number of compounds is too large we post in here the databases in smile format so the user should convert them into sdf. The Anchor atom is marked as Bromide. Therefore after the smile sdf convertion the user will hvae to substitute the Br atom to Du with a replace function in any text editor.

We recommend to the user to split the database computation in 4 runs that can be done in parallel. In order to do this:

A typical Shop database built using chemical building blocks and reactions contain scaffolds/fragments that are somehow too big for appropiate small bioisosteric changes, for example if the query fragment is a ketofurane we will probably not find any appropiate solution in those type of databases. Therefore, we have decided to generate a sample database starting from a collection of 250 hetrocycles. The aim of this database is not to provide synthetical feasability but to have access to small bioisosteric changes that can trigger the chemists imagination. This initial database is rather limited since the attachment are limited to only one type. We are now working in develping another DB with more attachment options.