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In this issue of tips & tricks we will demonstrate how easy it is to create a set of fragments from existing ligand data and index it with LeadIT.
These files are required for indexing:
- input mol2 file with 3D coordinates (test.mol2 supplied or your own file)
- shredding rules (*.ssp-file; ACSII; supplied here)
- ReCore or LeadIT executables (you should have that)
- a script (*.sh-file; supplied here)
The procedure for creating an index is a 3 step process, which is automatically triggered using the provided script, the step are as follows:
- Generate a so-called CUT-file which includes the fragments after applying the molecule shredding rules.
- Remove redundancies - both 3D (RMSD based) and 2D (SMILES based).
This creates a so-called PRUNED CUT-file.
- Index generation (=extraction of features) such as H-bond donor, H-bond acceptor, phenyl center etc.
If interested in this procedure and the commands to instigate each section then have a look at some more details.
- Generation of a cut file. In this step, on each molecule in the mol2 file cuts as specified in the .ssp file are annotated and stored in the so-called cut file. The command for doing this would look like this:
leadit --recore --molecules=<mol2-file> --cut-file=<name_of_cut_file>
--shredding-spec=<file.ssp>
- Pruning the cut file. Here, conformational duplicates of otherwise identical molecules are removed, if they are below the 1Å threshold.
leadit --recore --molecules=<mol2-file> --cut-file=<name_of_cut_file>
--pruned-cut-file=<name_of_pruned_file> --shredding-spec=<file.ssp>
- Generation of the index. Now the exit vectors and features are extracted from the fragments and stored in the index. For this step, the (unpruned) cut file is not needed any more
leadit --recore --pruned-cut-file=<name_of_pruned_file> --rsx=<index_name>
--feature-selection=<features_to_go_in_the_index, cp below> --verbose yes
Please follow the forthcoming instructions to create an index from the file test.mol2 or your own ?.mol2 file:
- Extract all the files in this download to a directory of your choice.
- Please edit buildindex.bat or buildindex.sh and change 'set recore=<PATH-TO-LEADIT>' so that ReCore is pointing to the point of your LeadIT executable.
- Run the script buildindex.bat or buildindex.sh; close any open sessions of LeadITs that may be open at the time.
- Then move at least the files
*.pcut
*.mol2
*.ssp
*.rsx
into the same directory of a local hard disk.
- Open LeadIT, select ReCore on the splash screen and then click on the highlighted circled link section in the picture below.
Now click on '...' on the respective green highlighted line of the RECORE_DB_FILENAME parameter to set the path to myindex.rsx.
- The new index has been selected for searching, perform any ReCore queries as normal, and enjoy your new ReCore index!
If you have any questions or require any further help then please do ask us.
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