Difference between revisions of "Fragment Library Generation"

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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.
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An example of an input file to generate a fragment library calling DOCK6:
 
An example of an input file to generate a fragment library calling DOCK6:
 
   
 
   
 
  conformer_search_type                                        flex
 
  conformer_search_type                                        flex
−
user_specified_anchor                                        no
 
−
limit_max_anchors                                            no
 
−
min_anchor_size                                              5
 
−
pruning_use_clustering                                      no
 
−
pruning_max_orients                                          100
 
−
pruning_orient_score_cutoff                                  100.0
 
−
pruning_max_conformers                                      75
 
−
pruning_conformer_score_cutoff                              100.0
 
−
use_clash_overlap                                            no
 
−
write_growth_tree                                            no
 
 
  write_fragment_libraries                                    yes
 
  write_fragment_libraries                                    yes
−
  fragment_library_prefix                                      ${SYSTEM}.fraglib
+
  fragment_library_prefix                                      fraglib
−
  fragment_library_freq_cutoff                                ${FREQ_CUTOFF}
+
  fragment_library_freq_cutoff                                1
 
  fragment_library_sort_method                                ${SORT_METHOD}
 
  fragment_library_sort_method                                ${SORT_METHOD}
 
  fragment_library_trans_origin                                no
 
  fragment_library_trans_origin                                no
 
  use_internal_energy                                          no
 
  use_internal_energy                                          no
−
  ligand_atom_file                                            ../001.files/${SYSTEM}.lig.multigridmin.mol2
+
  ligand_atom_file                                            /PATH/001.files/compound_library.mol2
 
  limit_max_ligands                                            no
 
  limit_max_ligands                                            no
 
  skip_molecule                                                no
 
  skip_molecule                                                no
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  minimize_ligand                                              no
 
  minimize_ligand                                              no
 
  atom_model                                                  all
 
  atom_model                                                  all
−
  vdw_defn_file                                                ../001.files/vdw.defn
+
  vdw_defn_file                                                /PATH/001.files/vdw.defn
−
  flex_defn_file                                              ../001.files/flex.defn
+
  flex_defn_file                                              /PATH/001.files/flex.defn
−
  flex_drive_file                                              ../001.files/flex_drive.tbl
+
  flex_drive_file                                              /PATH/001.files/flex_drive.tbl
 
  ligand_outfile_prefix                                        output
 
  ligand_outfile_prefix                                        output
 
  write_orientations                                          no
 
  write_orientations                                          no
 
  num_scored_conformers                                        1
 
  num_scored_conformers                                        1
 
  rank_ligands                                                no
 
  rank_ligands                                                no
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The input parameter "write_fragment_libraries" will print out the fragments generated through the process of flex docking.

Latest revision as of 15:00, 19 February 2018

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.

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