Rigid receptor

Generating targetfile detailed explanations

The agfr command is used to compute grids of affinity values for a given set of atom types. This calculation is performed using the AutoGrid4 software program. These affinity values are calculated on evenly spaced grid points for a 3D box (docking box) placed over the receptor’s site targeted for automated docking.

> agfr -r 4EK3_rec.pdbqt # this is the target protein for docking

 -l 4EK4_lig.pdbqt # this is a known ligand

 -o ligPocket # save result in ligPocket.trg

The receptor is specified using the –r/--receptor command line option. This option is required.

The position and size of the box can be specified in a variety of ways using the –b/--boxMode option. In this particular case we instruct agfr to create the box as the bounding box of a known ligand’s atom centers (-l/--ligand).

By default, a padding of 4Ā is added to every side of the bounding box. The padding value can be modified using the –P/--padding option. is added on every side.

The agfr command generates a target file with a .trg extension. This file will be saved under the name specified by the –o/--output command line option. When omitted, a unique and descriptive filename will be created automatically. The target file contains the calculated affinity maps, translational points for placing the ligand in sensible places in the docking box, and meta data about the gird size, position, spacing, receptor atoms involved, affinity maps, etc. These files can be inspected using the about command.

The translational points are computed using the AutoSite software program. This program will analyze affinity maps and cluster high affinity points to identify clusters of points modeling potential binding pockets. The –p/--pocketMode allows specifying how to handle multiple clusters of affinity points representing the pockets found in the docking box. Since this option is omitted here, all clusters are merged to create a single set of translational points.

By default, maps are computed for all AutoDock4 atom types. The list of atom types for which to compute affinity maps can be set using the –m/--mapTypes option.  Generating affinity maps for fewer atom types generates smaller target files and takes less time to perform the calculation. However, such a target file cannot be used for docking ligands containing atoms for which the target files does not contain the affinity map.

Running this command generates the following output (saved in 4EK3_rec_cmdline.log)

 

fiji:rib sanner$ $MGLTools2/1.0/bin/agfr -l 4EK4_lig.pdbqt -r 4EK3_rec.pdbqt -b ligand -P 5.0 -o 4EK3_rec_cmdline -m ligand

MSMSLIB 1.4.4 started on fiji.scripps.edu

Copyright M.F. Sanner (March 2000)

Compilation flags 

#################################################################

# If you used AGFR in your work, please cite:                   #

#                                                               #

# P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and     #

# M.F. Sanner                                                   #

# AutoDockFR: Advances in Protein-Ligand Docking with           #

# Explicitly Specified Binding Site Flexibility                 #

# PLoS Comput Biol 11(12): e1004586                             #

# DOI:10.1371/journal.pcbi.1004586                              #

#                                                               #

# <PAPER TO COME> and                                           #

#                                                               #

# P. Ananad Ravindranath and M.F. Sanner                        #

# AutoSite: an automated approach for pseudoligands prediction  #

# - From ligand binding sites identification to predicting key  #

# ligand atoms                                                  #

# Bioinformatics (2016)                                         #

# DOI:10.1093/bioinformatics/btw367                             #

#                                                               #

# Please see http://adfr.scripps.edu for more information.      #

#################################################################

 

Computing grids on fiji.scripps.edu a Darwin-14.3.0-x86_64-i386-64bit computer

Date Mon Nov 21 10:53:41 2016

 

loading receptor: 4EK3_rec.pdbqt

loading ligand: 4EK4_lig.pdbqt

 

set box using ligand

    Box center:    23.332    28.922    29.598

    Box length:    17.250    16.500    12.000

    Box size  :        46        44        32

    padding   :     4.000

    spacing   :     0.375

 

identifying pockets using AutoSite ....

    found 1 pockets

 

    pocket|  energy | # of |Rad. of | energy |   bns    | score 

    number|         |points|gyration|per vol.|buriedness|v*b^2/rg

    ------+---------+------+--------+--------+----------+---------

        1   -120.94   267    4.12     -0.45      0.85      46.85

    merging clusters ...

done. got 267 fill Points, in 1.01 (sec)

 

setting map types using: all to ['HS', 'Mg', 'HD', 'NA', 'Fe', 'Br', 'NS', 'A', 'C', 'Mn', 'G', 'F', 'I', 'H', 'J', 'N', 'Q', 'P', 'S', 'GA', 'Z', 'Zn', 'Cl', 'Ca', 'OA', 'SA', 'OS']

 

computing maps for center=(23.332 28.922 29.598) size=(17.250 16.500 12.000) dims=(46 44 32) ...

    267 points inside the box

 

    maps computed in 5.30 (sec)

making target file ligPocket.trg ...    done.

done. 7.20 (sec)

 

Explanations:

After reading the receptor and ligand a box is set up around the ligand with a padding 5.0

set box using ligand

    Box center:    23.332    28.922    29.598

    Box length:    17.250    16.500    12.000

    Box size  :        46        44        32

    padding   :     4.000

    spacing   :     0.375

this box is then used to run AutoSite to identify pockets (i.e. clusters of fill points) within this box.

The resulting clusters are reported in the table

identifying pockets using AutoSite ....

    found 1 pockets

 

    pocket|  energy | # of |Rad. of | energy |   bns    | score 

    number|         |points|gyration|per vol.|buriedness|v*b^2/rg

    ------+---------+------+--------+--------+----------+---------

        1   -120.94   267    4.12     -0.45      0.85      46.85

    merging clusters ...

done. got 267 fill Points, in 1.01 (sec)

the --pocketMode best option selects the best (and only) pocket in this case

The affinity maps are computed for all AutoDock4 atom types.

setting map types using: all to ['HS', 'Mg', 'HD', 'NA', 'Fe', 'Br', 'NS', 'A', 'C', 'Mn', 'G', 'F', 'I', 'H', 'J', 'N', 'Q', 'P', 'S', 'GA', 'Z', 'Zn', 'Cl', 'Ca', 'OA', 'SA', 'OS']

Next the maps and valid translational points are computed

computing maps for center=(23.332 28.922 29.598) size=(17.250 16.500 12.000) dims=(46 44 32) ...

    267 points inside the box

 

    maps computed in 6.40 (sec)

Note that some fill points identified by AutoSite might fall slightly outside the box. Such points are discarded reducing the number of translational points from 31 to 303. These points will be used by ADFR to place the ligand in the docking box during the search of the best docked pose for a given ligand.

By default, the original AutoGrid maps are saved in the target file. To trigger maps post-processing to remove translational points located inside the molecular surface and to create a potential gradient pointing form the core of the protein to the surface use -R (--processMaps) command line option.

Finally, a file containing the maps, as well as the receptor and translational points (along with meta data about the maps) is created.

    making target file ligPocket.trg ...    done.