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 or HPB

  • aromatic or ARM

  • h_bond or HBD

  • electrostatic or ELE

  • h_bond_donor or HBD_DON

  • h_bond_acceptor or HBD_ACC

  • electrostatic_positive or ELE_POS

  • electrostatic_negative or ELE_NEG

  • aromatic_facetoface or ARM_F2F

  • aromatic_edgetoface or ARM_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.