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 | + | 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 | ||
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write_fragment_libraries yes | write_fragment_libraries yes | ||
fragment_library_prefix fraglib | fragment_library_prefix fraglib | ||
| − | fragment_library_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 | ||
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.
