Perturbation site parameters

These are parameters to set up the region to perturb with PELE.

List of perturbation site parameters:

Warning

Note that some parameters should only be used to define the region to perturb when using specific packages. They are initial_site, final_site and center_of_interface. More information is provided in the corresponding sections for each parameter.

List of examples:

box-center

  • Description: The center of the perturbation box inside which the ligand will be perturbed.

  • Type: 3-dimensional array of Float

  • Default: it depends on the package

Warning

This parameter will prevail over the effects of other box-related parameters like initial_site, final_site and center_of_interface and its combination is usually not recommended.

Note

This parameter is set according to the Platform package that is chosen since it has a strong connection with the type of simulation that is pursued. However, if this parameter is set, it will prevail over the default settings of any package.

Note

Note that, currently, we only support a spherical box.

Note

When custom boxes are set in a site_finder simulation, they change the behaviour of the package. Thus, instead of exploring the entire protein surface, the search will cover the custom box that is defined. You can check Example 2 to get more details about this strategy.

See also

initial_site, final_site, center_of_interface, packages, Example 1, Example 2

box-radius

  • Description: The radius, in angstroms, of the perturbation box inside which the ligand will be perturbed.

  • Type: Integer

  • Default: it depends on the package

Warning

This parameter will prevail over the effects of other box-related parameters like initial_site, final_site and center_of_interface and its combination is usually not recommended.

Note

This parameter is set according to the Platform package that is chosen since it has a strong connection with the type of simulation that is pursued. However, if this parameter is set, it will prevail over the default settings of any package.

Note

Note that, currently, we only support a spherical box.

Note

When custom boxes are set in a site_finder simulation, they change the behaviour of the package. Thus, instead of exploring the entire protein surface, the search will cover the custom box that is defined. You can check Example 2 to get more details about this strategy.

See also

initial_site, final_site, center_of_interface, packages, Example 1, Example 2

initial_site

  • Description: Selection of a protein atom that is near a good starting point for the simulation. The Platform will place the ligand as close as possible to this position.

  • Type: Atom selection, Character:Integer:String

  • Default: None

Warning

This parameter should only be set when running the out_in package.

Note

This parameter must be used along with final_site in order to let the Platform properly define the perturbation box.

See also

final_site, packages, Example 3, Out –> In tutorial

final_site

  • Description: Selection of a protein atom that is near the cavity that we want to visit. The Platform will build a perturbation box according to initial_site and final_site accordingly.

  • Type: Atom selection, Character:Integer:String

  • Default: None

Warning

This parameter should only be set when running the out_in package.

Note

This parameter must be used along with final_site in order to let the Platform properly define the perturbation box.

See also

initial_site, packages, Example 3, Out –> In tutorial

center_of_interface

  • Description: Selection of a protein atom that is centered in the protein interface that we want the ligand to explore. The Platform will generate initial structures placing the ligand near this region and it will build a perturbation box to explore it properly.

  • Type: Atom selection, Character:Integer:String

  • Default: None

Warning

This parameter should only be set when running the PPI package.

See also

packages, Example 4, PPI tutorial

Example 1

In this example we set an induced fit docking simulation with 30 computation cores. We also set a custom perturbation box. The default box used in an induced fit docking is to center a spherical box of 6-angstrom radius on the center of mass of the ligand. However, we can change its center and radius with values of our choice using box_radius and box_center parameters.

# Required parameters
system: 'system.pdb'
chain: 'L'
resname: 'LIG'

# General parameters
cpus: 30
seed: 2021

# Package selection
induced_fit_fast: True

# Perturbation site parameters
box_radius: 5
box_center:
  - 21
  - -3
  - 5

Example 2

In this example we set a site finder simulation with 60 computation cores. By default, this package will place our ligand all over the protein to promote the exploration of the whole surface. However, in case that we are interested in exploring a particular subregion of its surface, we can define a custom box that only covers it. Then, the Platform will spawn structures inside that box and will guarantee that the ligand does not exit it during the simulation.

# Required parameters
system: 'system.pdb'
chain: 'L'
resname: 'LIG'

# General parameters
cpus: 60
seed: 2021

# Package selection
site_finder: True

# Perturbation site parameters
box_radius: 20
box_center: 'A:241:CA'

Example 3

In this example we set an out –> in docking simulation with 60 computation cores. When using this package, we also need to set initial and final sites in order to properly define the starting point and the region to explore during the migration of our ligand.

# Required parameters
system: 'system.pdb'
chain: 'L'
resname: 'LIG'

# General parameters
cpus: 60
seed: 2021

# Package selection
out_in: True

# Perturbation site parameters
initial_site: "A:43:O"
final_site: "A:104:CD"

Example 4

In this example we set an out –> in docking simulation with 60 computation cores. When using this package, we also need to set initial and final sites in order to properly define the starting point and the region to explore during the migration of our ligand.

# Required parameters
system: 'system.pdb'
chain: 'L'
resname: 'LIG'

# General parameters
cpus: 60
seed: 2021

# Package selection
ppi: True

# Perturbation site parameters
center_of_interface: "A:206:O"