# Chemical group transformations¶

SILCS-MC ligand optimization and SSFEP both entail computations on derivatives of a parent ligand. Additionally, the user may wish to perform SILCS docking using a series of structures chemically related to a reference compound (i.e. parent ligand). Therefore, a task common to these use cases is that of performing chemical group transformations on a parent ligand to create a series of chemically-related compounds.

The SilcsBio GUI provides an intuitive way to handle this task directly in the context of SILCS-MC ligand optimization (see Running SILCS-MC ligand optimization from the SilcsBio GUI) and SSFEP (see SSFEP simulation from the GUI). You can also use the SilcsBio GUI to perform chemical transformations independently of any other task by choosing Modify ligand for SILCS-MC/SSFEP from the Home page. Output Mol2 files will be saved to a directory of your choosing on the machine where you are running the SilcsBio GUI.

It is also possible to perform chemical group transformations using the command line interface, as described below.

You will need to create a text file modifications.txt with instructions listing the desired modifications to your parent ligand.

Three types of modifications can be performed, as listed in the table.

Command

Modification

JOIN

Join a fragment (mol2) to the parent at a defined site

REPL

Replace an atom at a defined site on the parent with a fragment (mol2)

MUDE

Change an atom at a defined site on the parent to another atom-type

An example ligand modification input file is povided with your SilcsBio server software, ${SILCSBIODIR}/examples/ssfep/modification.txt. For details on how to modify and process this file to create Mol2 files containing modifications to your parent ligand, run the following command: ${SILCSBIODIR}/programs/chemmod -h


Your SilcsBio server software comes with a large number of fragments in Mol2 format that can be added/joined to your parent ligand. These fragments are found in: