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apo2ph4_howto.rtf
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HYPERLINK "http://openbabel.org/wiki/Main_Page"}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 {\*\datafield
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\rtlch\fcs1 \af44 \ltrch\fcs0 \cs15\ul\cf9\lang255\langfe2052\langnp255\insrsid16653735 http://openbabel.org/wiki/Main_Page}}}\sectd \ltrsect\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj {\rtlch\fcs1 \af44 \ltrch\fcs0
\lang3079\langfe2052\langnp3079\insrsid16653735\charrsid2960414 )
\par }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 Knime (4.1.2 or newer) }{\field{\*\fldinst {\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 HYPERLINK "https://www.knime.com/downloads"}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 {\*\datafield
00d0c9ea79f9bace118c8200aa004ba90b0200000003000000e0c9ea79f9bace118c8200aa004ba90b40000000680074007400700073003a002f002f007700770077002e006b006e0069006d0065002e0063006f006d002f0064006f0077006e006c006f00610064007300000000}}}{\fldrslt {\rtlch\fcs1 \af44
\ltrch\fcs0 \cs15\ul\cf9\lang255\langfe2052\langnp255\insrsid16653735 https://www.knime.com/downloads}}}\sectd \ltrsect\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj {\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
\par LigandScout Knime exensions (available as a KNIME Partner extension)
\par AutoDock4 including AutoGrid4 (}{\field{\*\fldinst {\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 HYPERLINK "https://autodock.scripps.edu/download-autodock4/"}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 {\*\datafield
00d0c9ea79f9bace118c8200aa004ba90b0200000003000000e0c9ea79f9bace118c8200aa004ba90b62000000680074007400700073003a002f002f006100750074006f0064006f0063006b002e0073006300720069007000700073002e006500640075002f0064006f0077006e006c006f00610064002d00610075007400
6f0064006f0063006b0034002f00000000}}}{\fldrslt {\rtlch\fcs1 \af44 \ltrch\fcs0 \cs15\ul\cf9\lang255\langfe2052\langnp255\insrsid16653735 https://autodock.scripps.edu/download-autodock4/}}}\sectd \ltrsect
\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj {\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 )
\par AutoDock Vina (}{\field{\*\fldinst {\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 HYPERLINK "https://vina.scripps.edu/downloads/"}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 {\*\datafield
00d0c9ea79f9bace118c8200aa004ba90b0200000003000000e0c9ea79f9bace118c8200aa004ba90b48000000680074007400700073003a002f002f00760069006e0061002e0073006300720069007000700073002e006500640075002f0064006f0077006e006c006f006100640073002f00000000}}}{\fldrslt {
\rtlch\fcs1 \af44 \ltrch\fcs0 \cs15\ul\cf9\lang255\langfe2052\langnp255\insrsid16653735 https://vina.scripps.edu/downloads/}}}\sectd \ltrsect\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj {\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 )
\par
\par }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 Required to be accessible via $PATH:}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
\par MGLTools Utilities (e.g. in [\'85]/mgltools/MGLToolsPckgs/AutoDockTools/Utilities24/)
\par OpenBabel
\par Knime
\par AutoDock4
\par AutoDock Vina
\par
\par
\par }{\rtlch\fcs1 \ab\af44\afs28 \ltrch\fcs0 \cs16\b\fs28\insrsid16653735 Quickstart guide}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
\par
\par The workflow comprises three steps (scripts) where one of them is optional. If desired}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid5643065 ,}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 these scripts may be }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid4923549
executed in succession using a bash script }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 to require no intervention after a binding pocket is selected.
\par
\par 1. (Optional) }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 apo2ph4_define_binding_site.py}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
\par If a binding site is defined by specifying cartesian coordinates }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735\charrsid3829177 apo2ph4_define_binding_site.py}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
must be run beforehand. It takes one PDB file and the x,y and z coordinates as positional arguments. This script removes all ligands, }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid8938710 ions,}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
and solvent molecule before placing a dummy molecule at the defined coordinates.
\par
\par For example:
\par
\par }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\highlight16\insrsid16653735 apo2ph4_define_binding_site.py [protein].pdb 141.021 55.154 89.114}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
\par
\par This generates }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 [protein]_prepared.pdb }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 in the same folde}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid4923549 r as the input PDB.}{\rtlch\fcs1 \af44
\ltrch\fcs0 \insrsid16653735
\par
\par This file may also be opened in LigandScout which now recognizes the binding site due to placement of the dummy molecule.
\par
\par 2) }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 apo2ph4_prepare_and_dock.sh }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
\par The second part of the workflow is a bash script that takes two positional arguments, for example:
\par
\par }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\highlight16\insrsid16653735 sh apo2ph4_prepare_and_dock.sh [fragment_library].sdf [protein]_prepared.pdb}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
\par }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 \line [fragment_library].sdf }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
should contain the fragment database with 3D-coordinates in SDF format (this database may for example be prepared by energy minimizing a fragment library lacking 3D coordinates in LigandScout and then saving it in SDF format).
\par }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 [protein]_prepared.pdb }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
was either prepared beforehand (step 1) or should be a PDB file only containing a single ligand that defines the binding site (other ligands, ions and solvent mole
cules must be removed). The script should ideally be called from the directory that contains the PDB file .
\par
\par The script generates a combined LigandScout *.pml file as }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 ./pharmacophores/pharmacophores.pml}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 in the current working directory. The necessary grid
energy files are placed in the parent folder as *.map (e.g. }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 receptor.C.map}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 ) files which also contains the }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0
\b\insrsid16653735 feature_count.txt }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 file required for subsequent steps.
\par
\par }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 Additional notes:}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
\par It should be noted that this executes knime in batch mode with pre-set memory parameters, if not enough resources are available or for optimal performance the following parameters of the last line of }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735
apo2ph4_prepare_and_dock.sh }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 should be modified }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735\charrsid9925990 \'93}{\rtlch\fcs1 \af44 \ltrch\fcs0 \highlight16\insrsid16653735\charrsid9925990
-vmargs -Xmx32000m -Xms10048m}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 \'93
\par -Xmx32000m defines the maximum available memory (in this case 32 GB) and -Xms10048m defines the initial memory reserved (in this case 10 GB)
\par
\par Intermediate files such as docked poses, mock ligand/protein complexes are stored in }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 ./tempdock/}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 .
\par Contents of }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 ./tempdock/ }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 are not required for subsequent steps and g
et only saved for debugging purposes. As this occupies a lot of space (~500 MB for 200 fragments) it is recommended that a \'93}{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\highlight16\insrsid16653735\charrsid9925990 rm -rf ./tempdock/}{\rtlch\fcs1 \ab\af44
\ltrch\fcs0 \b\insrsid16653735 }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 \'94}{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
is added to the end of the script should these files not be desired.
\par \line Vina docking parameters are hardcoded, these may be changed by modifying the }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 /scripts/write_vina_conf.py }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 file in the workflow scripts directory
\par
\par 3) }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 apo2ph4_generate_ph4.py}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
\par The last step of the workflow generates a final pharmacophore model and requires the }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 pharmacophores.pml}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 , }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0
\b\insrsid16653735 grid map}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 and }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 feature_count.txt }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 files generated by the previous step.
\par
\par The number of pharmacophore features, energy thresholds as well as other settings may be specified by optional parameters.
\par Call }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\highlight16\insrsid16653735 apo2ph4_generate_ph4.py -h}{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735 }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 to see all available parameters for advanced usage
\par
\par basic example (mandatory arguments only):
\par
\par }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\highlight16\insrsid16653735 apo2ph4_generate_ph4.}{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\highlight16\insrsid2960414 py}{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\highlight16\insrsid9925990\charrsid9925990 }{\rtlch\fcs1
\ab\af44 \ltrch\fcs0 \b\highlight16\insrsid9925990 -i pharmacophores.pml -o my_ph4.pml -g ../}{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735
\par }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 advanced example:
\par }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\highlight16\insrsid16653735 apo2ph4_generate_ph4.py -i pharmacophores.pml -o my_ph4.pml -g ../ -n 8 --name "my pharmacophore model" -H 5 --H_energy -0.6 -v}{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735
\par }{\rtlch\fcs1 \ab\af44 \ltrch\fcs0 \b\insrsid16653735
\par }{\rtlch\fcs1 \af44 \ltrch\fcs0 \insrsid16653735 It is recommended to examine the final pharmacophore model visually by means of LigandScout to make sure no features have been placed outside the actual binding pocket.
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