Fragment Library Generation
Fragment Library Generation is achieved through flex docking. During flex docking, DOCK6 cleaves the molecule along rotatable bonds and stores each of the fragments as a sidechain (one attachment point), linker (two attachment points), or a scaffold (three or more attachment points). Using this fragment library DOCK6 reassembles the molecule based on the produced torsion environment. In the process of cleaving the rotatable bonds, DOCK6 also creates a torsion table that holds all atom connectivity information. No bonds not found in the torsion tables will be formed in reassembling the molecule. The torsion table is also used for increasing chemical feasiblity of de novo design molecules.
An example of an input file to generate a fragment library calling DOCK6:
conformer_search_type flex write_fragment_libraries yes fragment_library_prefix fraglib fragment_library_freq_cutoff 1 fragment_library_sort_method ${SORT_METHOD} fragment_library_trans_origin no use_internal_energy no ligand_atom_file /PATH/001.files/compound_library.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no use_database_filter no orient_ligand no bump_filter no score_molecules no minimize_ligand no atom_model all vdw_defn_file /PATH/001.files/vdw.defn flex_defn_file /PATH/001.files/flex.defn flex_drive_file /PATH/001.files/flex_drive.tbl ligand_outfile_prefix output write_orientations no num_scored_conformers 1 rank_ligands no
The input parameter "write_fragment_libraries" will print out the fragments generated through the process of flex docking.