View source for 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                                 10
 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.