==History and Changes==
[[DOCK 3.5 Changes]]
[[DOCK 3.6]]

Here is the DOCK 3.5 manual from 1994: [http://wiki.bkslab.org/images/4/4e/Dock3_5refman.pdf DOCK 3.5 Manual]

Note that DOCK 3.6 now uses Qnifft as a alternative to Delphi see [[Qnifft DOCK 3.6 conversion]] for dicussion of this change.

Using Qnifft grids with DOCK 3.5.54 may result in unresonably high electrostatic energies. So be aware of the DOCK version being used and the Electrostatic grids generation method.

==Compilation==

*[[Dock development]]

*[[How to compile DOCK]]

==DOCK Tools==
[[Docking tools]]

[[Flexibase Format]]

= Programs, Files, and Protocols=

To run DOCK 3.6 for small molcule docking and virtual screening, you need the following:
* Receptor grid (generated with delphi)
* Spheres (coloured with )
* database file containing conformational expantion of your small molecules.

=DOCK 3 INPUT FILE and Parameters=

[[INDOCK for DOCK 3.6]]

[[MPose]]

[[Dock Ligand Clustering]]

Here is an example input file:

DOCK 3.5 parameter
################################################.1.A#
######### DOCK 3.6 INPUT PARAMETER FILE #############
##############################################INPUT##
#
receptor_sphere_file ../../sph/match2.sph
cluster_numbers 1
ligand_atom_file split_database_index
output_file_prefix test.
random_seed 777
#
##############################MATCHING###############
#
distance_tolerance 1.2
nodes_maximum 4
nodes_minimum 3
ligand_binsize 0.3
ligand_overlap 0.1
receptor_binsize 0.3
receptor_overlap 0.1
bump_maximum 1
focus_cycles 0
focus_bump 0
focus_type energy
critical_clusters no
#
##############################COLORING###############
#
chemical_matching yes
case_sensitive no
# ligand color, receptor color
match positive negative
match positive negative_or_acceptor
match positive not_neutral
match negative positive
match negative positive_or_donor
match negative not_neutral
match donor acceptor
match donor donacc
match donor negative_or_acceptor
match donor neutral_or_acceptor_or_donor
match donor not_neutral
match acceptor donor
match acceptor donacc
match acceptor positive_or_donor
match acceptor neutral_or_acceptor_or_donor
match acceptor not_neutral
match neutral neutral
match neutral neutral_or_acceptor_or_donor
match ester_o donor
match ester_o donacc
match ester_o positive_or_donor
match ester_o not_neutral
match amide_o donor
match amide_o donacc
match amide_o positive_or_donor
match amide_o not_neutral
#
##############################SEARCH MODE###############
#
ligand_desolvation volume
ratio_minimum 0.0
atom_minimum 5
atom_maximum 60
number_save 500
molecules_maximum 300000
restart_interval 10000
initial_skip 0
timeout 20
#
##############################SCORING###################
#
solvmap_file ../../grids/solvmap_sev
delphi_file ../../grids/rec+sph2.qnifft.phi
chemgrid_file_prefix ../../grids/chem
vdw_parameter_file ../../grids/vdw.parms.amb.mindock
check_clashes yes
remove_positive_solvation no
vdw_maximum 1.0e10
electrostatic_scale 1.0
vdw_scale 1.0
#
##############################MINIMIZATION##############
#
minimize yes
minimization_max 1.0e15
check_degeneracy no
simplex_iterations 1000
simplex_convergence 0.1
simplex_restart 1.0
simplex_initial_translation 0.2
simplex_initial_rotation 5.0

==Parameters==
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"
|- style="background:lightgreen"
! style="width 30%" !|Parameter Name
! style="width:70%" !|Discription
|-
|receptor_sphere_file
|Sphere file.
|-
|cluster_numbers
|This has to do with the sphere clusters.
|-
|ligand_atom_file
| the text file that contains list of 'db.gz' files. Eg. split_database_index
|-
|output_file_prefix
|Output file prefix for the test.
|-
|random_seed
|The Simplex Minimizer requiers a random seed integer. eg.777
|-
|}

===SEARCH MODE===

{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"
|- style="background:red"
! style="width 30%" !|Parameter Name
! style="width:70%" !|Discription
|-
| mode
| This parameter has be deprecated. Only the "search" mode is curently used. the "single" mode, which alowed multiple ligand conformations to be saved, was broken and was removed from DOCK 3.6. This fuctionality is in version 3.5 (Mpose binary [[MPose]]). The ligand clustering [[Dock Ligand Clustering]] code also alows for multiple conformations to be saved.
|-

{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"
|- style="background:lightgreen"
! style="width 30%" !|Parameter Name
! style="width:70%" !|Discription
|-
| ligand_desolvation
| volume
|-
| ratio_minimum
| 0.0
|-
| atom_minimum
| 5
|-
| atom_maximum
| 60
|-
| number_save
| 500 (Maxium is 5000)
|-
| molecules_maximum
| 300000
|-
| restart_interval
| 10000
|-
| initial_skip
| 0
|-
| timeout
| 20
|-
|}

=DOCK 3 Scoring Function=

solvmap_file ../../grids/solvmap_sev
delphi_file ../../grids/rec+sph2.qnifft.phi
chemgrid_file_prefix ../../grids/chem
vdw_parameter_file ../../grids/vdw.parms.amb.mindock
check_clashes yes
remove_positive_solvation no
vdw_maximum 1.0e10
electrostatic_scale 1.0
vdw_scale 1.0

[[Category:DOCK]]

2012-09-19T23:32:07Z

Tbalius:

This is intended for internal use for the BKS lab members.

==Overveiw==
Everytime a new Chembl comes out we need to process it.

* Extract the following information from MYSQL into files and bins.

==Extract==

This is currently done in Bet's Directories:
~bet/ChEMBL/chembl14/

The "scripts/mysql_export.sh" is a shell script that calls information that has been loaded in to the MySQL data base on SGEHEAD of the BKSLB cluster.

syntax: mysql_export.sh chembl_db_name [F|B|A]

chembl_db_name chemble databas file, for example chembl14 is release
F -- Functional Data: for example, cell assays to efficacy ( life span of a mouse).
B -- Binding Datd: ki, kd,
A -- Affinity: ??

To do this run the following:

>> scripts/mysql_export.sh chembl14 B

== process data==
Next we run the following script to process the data into the correct format:

>> scripts/run_after_export.py -h
usage: run_after_export.py [options] activities.txt outfile

options:
-h, --help show this help message and exit
-m X, --maxaffinity=X
Only include affinities up to X nM (default 10000)
-f, --funct Work with functional data (default binding data)

== make input for SEA ==

makeChEMBLsets.py is a script that builds set.gz and smi.gz files from ChEMBL exports for [[SEA]] analisis

>> scripts/makeChEMBLsets.py

'usage: scripts/makeChEMBLsets.py [options] targets.txt smiles.txt activities.txt'

'-s','--swissprot','Read Uniprot/Swiss-Prot IDs from FILE '
'-t','--trembl','Read Uniprot/TrEMBL IDs from FILE

'-p','--pickle','Read Uniprot/Swiss-Prot IDs from dictionary in Pickle FILE
'-o','--output''Basename to generate output files and directories',
'-b','--bin','Generate binned sets',
targetsFile,smilesFile,activitiesFile = args

Chembl processing protocol

2012-09-19T23:25:12Z

Tbalius:

Chembl processing protocol

2012-09-19T23:02:27Z

Tbalius:

Chembl processing protocol

2012-09-19T22:57:31Z

Tbalius:

This is intended for internal use for the BKS lab members.

Everytime a new Chembl comes out we need to process it.

* Exstact the following information from MYSQL into files and bins.

The "scripts/mysql_export.sh" is a shell script that calls information that has been loaded in to the MySQL data base on SGEHEAD of the BKSLB cluster.

syntax: mysql_export.sh chembl_db_name [F|B|A]

chembl_db_name chemble databas file, for example chembl14 is release
F -- Functional Data: for example, cell assays to efficacy ( life span of a mouse).
B -- Binding Datd: ki, kd,
A -- Affinity: ??

To do this run the following:

>> scripts/mysql_export.sh chembl14 B

2012-09-05T16:36:19Z

Tbalius:

=Compilation=

= Programs, Files, and Protocols=

To run DOCK 3.6 for small molcule docking and virtual screening, you need the following:
* Receptor grid (generated with delphi)
* Spheres (coloured with )
* database file containing conformational expantion of your small molecules.

=DOCK 3 INPUT FILE and Parameters=

Here is an example input file:

DOCK 3.5 parameter
################################################.1.A#
######### DOCK 3.6 INPUT PARAMETER FILE #############
##############################################INPUT##
#
receptor_sphere_file ../../sph/match2.sph
cluster_numbers 1
ligand_atom_file split_database_index
output_file_prefix test.
random_seed 777
#
##############################MATCHING###############
#
distance_tolerance 1.2
nodes_maximum 4
nodes_minimum 3
ligand_binsize 0.3
ligand_overlap 0.1
receptor_binsize 0.3
receptor_overlap 0.1
bump_maximum 1
focus_cycles 0
focus_bump 0
focus_type energy
critical_clusters no
#
##############################COLORING###############
#
chemical_matching yes
case_sensitive no
# ligand color, receptor color
match positive negative
match positive negative_or_acceptor
match positive not_neutral
match negative positive
match negative positive_or_donor
match negative not_neutral
match donor acceptor
match donor donacc
match donor negative_or_acceptor
match donor neutral_or_acceptor_or_donor
match donor not_neutral
match acceptor donor
match acceptor donacc
match acceptor positive_or_donor
match acceptor neutral_or_acceptor_or_donor
match acceptor not_neutral
match neutral neutral
match neutral neutral_or_acceptor_or_donor
match ester_o donor
match ester_o donacc
match ester_o positive_or_donor
match ester_o not_neutral
match amide_o donor
match amide_o donacc
match amide_o positive_or_donor
match amide_o not_neutral
#
##############################SEARCH MODE###############
#
ligand_desolvation volume
ratio_minimum 0.0
atom_minimum 5
atom_maximum 60
number_save 500
molecules_maximum 300000
restart_interval 10000
initial_skip 0
timeout 20
#
##############################SCORING###################
#
solvmap_file ../../grids/solvmap_sev
delphi_file ../../grids/rec+sph2.qnifft.phi
chemgrid_file_prefix ../../grids/chem
vdw_parameter_file ../../grids/vdw.parms.amb.mindock
check_clashes yes
remove_positive_solvation no
vdw_maximum 1.0e10
electrostatic_scale 1.0
vdw_scale 1.0
#
##############################MINIMIZATION##############
#
minimize yes
minimization_max 1.0e15
check_degeneracy no
simplex_iterations 1000
simplex_convergence 0.1
simplex_restart 1.0
simplex_initial_translation 0.2
simplex_initial_rotation 5.0

==Parameters==
{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"
|- style="background:lightgreen"
! style="width 30%" !|Parameter Name
! style="width:70%" !|Discription
|-
|receptor_sphere_file
|Sphere file.
|-
|cluster_numbers
|??
|-
|ligand_atom_file
| the text file that contains list of 'db.gz' files. Eg. split_database_index
|-
|output_file_prefix
|Output file prefix for the test.
|-
|random_seed
|The Simplex Minimizer requiers a random seed integer. eg.777
|-
|}

===SEARCH MODE===

{| border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:90%"
|- style="background:lightgreen"
! style="width 30%" !|Parameter Name
! style="width:70%" !|Discription
|-
| ligand_desolvation
| volume
|-
| ratio_minimum
| 0.0
|-
| atom_minimum
| 5
|-
| atom_maximum
| 60
|-
| number_save
| 500 (Maxium is 5000)
|-
| molecules_maximum
| 300000
|-
| restart_interval
| 10000
|-
| initial_skip
| 0
|-
| timeout
| 20
|-
|}

=DOCK 3 Scoring Function=

[[Category:DOCK]]

Install SEA

2012-08-30T20:47:35Z

Tbalius:

Install SEA

2012-08-30T20:25:08Z

Tbalius:

Install SEA

2012-08-30T20:24:17Z

Tbalius: