Advanced Usage¶
Customize Bitstring by Omitting Specific Interactions¶
It is possible to omit certain interaction(s) in selected residue(s).
This will cause PyPLIF HIPPOS to replace the omitted interaction in the bitstring
with n
character (eg. from 1010001
to 1n10001
). As a consequence, the omitted
interaction will not be included in similarity calculation. This is done by
removing the omitted interaction bit both in the target and the reference bitstring. As
a result the similarity coefficient could be different from the default one.
To omit interaction just add the following line to the configuration file:
omit_interaction interaction_type residue_name [single or multiple]
where interaction_type
is one of the following value:
hydrophobic
orHPB
aromatic
orARM
h_bond
orHBD
electrostatic
orELE
h_bond_donor
orHBD_DON
h_bond_acceptor
orHBD_ACC
electrostatic_positive
orELE_POS
electrostatic_negative
orELE_NEG
aromatic_facetoface
orARM_F2F
aromatic_edgetoface
orARM_E2F
As for the residue_name
it could be one or more residue name. Here is
one example of a valid omit_interaction definition:
omit_interaction hydrophobic ARG223
As a quick start here is three different scenario on omitting interaction.
Omit single interaction¶
This configuration file (examples-input/08-na_omit_interaction/vina-omit-simple.txt) shows how you can omit hydrophobic interaction on ARG223 residue
docking_method vina # plants or vina
docking_conf ../03-na_vina/vina-003.conf
similarity_coef tanimoto mcconnaughey
full_ref 00000100000000000000000000000000000100000000000001000000000000010000001000000000000000000001000000000000000000000000000000101000000000000000000101000000000010000 00010101000000000000000000000000000100000000000001010000000000010000001000000000000010000000000000000000000001011000001000001000000000000000000101000000000000000 00010101000000100000000000000000000100000000000001010000000000010000001000000000000010000001000000000000010000000000100000101010000000000000000001000000000000000
omit_interaction hydrophobic ARG223
residue_name ARG116 GLU117 LEU132 LYS148 ASP149 ARG150 ARG154 TRP177 SER178 ILE221 ARG223 THR224 GLU226 ALA245 HIS273 GLU275 GLU276 ARG292 ASP294 GLY347 ARG374 TRP408 TYR409
residue_number 40 41 56 72 73 74 78 101 102 145 147 148 150 169 197 199 200 216 218 271 298 332 333
full_outfile omit-simple.csv
sim_outfile omit-simple-similarity.csv
logfile omit-simple.log
Here is the excerpt from the bitstring output using the above configuration file
129821_1 -6.9 0000000100000000000000000000100000010010000000000000000000000001000000n000000000000010000001000000000000000000000000000000100000000010000000000100000000000001000
129821_2 -6.8 0000000000000000000000000000000000010000000000000101000000000001000000n000000000000000000001000000000000000001010000000000100000000010000000000000000000000001000
129821_3 -6.6 0000000000000000000000000000100000110000000000000101000000000001000000n000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000
129821_4 -6.4 0000000000000000000000000000100010000000000000000000000000000001000000n000000000000000000001000000000000000000010000101000000000000000000000000000000000000000000
129821_5 -6.2 0000000000000000000000000000100000010000000000000101000000000001000000n000000000000000000001000000000000000000000000000000000000001010000000000100000000000001000
Notice that there is an n
character that replace one of the bit.
Omit single interaction in several residue¶
The following configuration file (examples-input/08-na_omit_interaction/vina-omit-residues.txt) shows how you can omit hydrophobic interaction on ARG150 TRP177 ARG223 residues
docking_method vina # plants or vina
docking_conf ../03-na_vina/vina-003.conf
similarity_coef tanimoto mcconnaughey
full_ref 00000100000000000000000000000000000100000000000001000000000000010000001000000000000000000001000000000000000000000000000000101000000000000000000101000000000010000 00010101000000000000000000000000000100000000000001010000000000010000001000000000000010000000000000000000000001011000001000001000000000000000000101000000000000000 00010101000000100000000000000000000100000000000001010000000000010000001000000000000010000001000000000000010000000000100000101010000000000000000001000000000000000
omit_interaction hydrophobic ARG150 TRP177 ARG223
residue_name ARG116 GLU117 LEU132 LYS148 ASP149 ARG150 ARG154 TRP177 SER178 ILE221 ARG223 THR224 GLU226 ALA245 HIS273 GLU275 GLU276 ARG292 ASP294 GLY347 ARG374 TRP408 TYR409
residue_number 40 41 56 72 73 74 78 101 102 145 147 148 150 169 197 199 200 216 218 271 298 332 333
full_outfile omit-residues.csv
sim_outfile omit-residues-similarity.csv
logfile omit-residues.log
Here is the excerpt from the bitstring output using the above configuration file
129821_1 -6.9 00000001000000000000000000001000000n0010000000000n00000000000001000000n000000000000010000001000000000000000000000000000000100000000010000000000100000000000001000
129821_2 -6.8 00000000000000000000000000000000000n0000000000000n01000000000001000000n000000000000000000001000000000000000001010000000000100000000010000000000000000000000001000
129821_3 -6.6 00000000000000000000000000001000001n0000000000000n01000000000001000000n000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000
129821_4 -6.4 00000000000000000000000000001000100n0000000000000n00000000000001000000n000000000000000000001000000000000000000010000101000000000000000000000000000000000000000000
129821_5 -6.2 00000000000000000000000000001000000n0000000000000n01000000000001000000n000000000000000000001000000000000000000000000000000000000001010000000000100000000000001000
Notice that there are three n
, each of them replace hydrophobic interaction in one residue.
Omit more than one interaction¶
And here is how you can omit more than one interaction, this configuration file (examples-input/08-na_omit_interaction/vina-omit-interactions.txt) shows you how to omit the hydrophobic interaction on ARG223 and hydrogen bond (both as donor and acceptor) on ARG292
docking_method vina # plants or vina
docking_conf ../03-na_vina/vina-003.conf
similarity_coef tanimoto mcconnaughey
full_ref 00000100000000000000000000000000000100000000000001000000000000010000001000000000000000000001000000000000000000000000000000101000000000000000000101000000000010000 00010101000000000000000000000000000100000000000001010000000000010000001000000000000010000000000000000000000001011000001000001000000000000000000101000000000000000 00010101000000100000000000000000000100000000000001010000000000010000001000000000000010000001000000000000010000000000100000101010000000000000000001000000000000000
omit_interaction hydrophobic ARG223
omit_interaction h_bond ARG292
residue_name ARG116 GLU117 LEU132 LYS148 ASP149 ARG150 ARG154 TRP177 SER178 ILE221 ARG223 THR224 GLU226 ALA245 HIS273 GLU275 GLU276 ARG292 ASP294 GLY347 ARG374 TRP408 TYR409
residue_number 40 41 56 72 73 74 78 101 102 145 147 148 150 169 197 199 200 216 218 271 298 332 333
full_outfile omit-interactions.csv
sim_outfile omit-interactions-similarity.csv
logfile omit-interactions.log
Here is the excerpt from the bitstring output using the above configuration file
129821_1 -6.9 0000000100000000000000000000100000010010000000000000000000000001000000n000000000000010000001000000000000000000000000000000nn0000000010000000000100000000000001000
129821_2 -6.8 0000000000000000000000000000000000010000000000000101000000000001000000n000000000000000000001000000000000000001010000000000nn0000000010000000000000000000000001000
129821_3 -6.6 0000000000000000000000000000100000110000000000000101000000000001000000n000000000000000000001000000000000000000000000000000nn0000000000000000000000000000000000000
129821_4 -6.4 0000000000000000000000000000100010000000000000000000000000000001000000n000000000000000000001000000000000000000010000101000nn0000000000000000000000000000000000000
129821_5 -6.2 0000000000000000000000000000100000010000000000000101000000000001000000n000000000000000000001000000000000000000000000000000nn0000001010000000000100000000000001000
Notice that there are three n
, the first one is replacing the hydrophobic interaction
on ARG223, while the second and third both are replacing the hydrogen bond interaction on
ARG292.