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Virtual Screening

Pharmacelera Extension for KNIME Workbench version 1.0.0.v202004161715 by Pharmacelera

The virtual screening module enables you to perform a virtual screening campaign.

Options

License file

Use this option to select the license file. To run the Virtual Screening Node is necessary to have a valid license file to allow you to run simulations. To obtain a valid license file, please, contact Pharmacelera (contact@pharmacelera.com).

Alignment type
  • Field based
    Molecule alignment is performed maximizing field similarity using the molecular moments of the selected fields of interaction.
  • Disabled
    This option disables molecular alignment. It can be selected to use user-provided alignments (e.g. using alignments from a docking).
  • Structure based
    A substructure alignment is performed maximizing field similarity.
  • Field based + Montecarlo
    This option performs the molecular alignment of the field based option and then refines it using a Montecarlo optimization to maximize field similarity among the reference and the aligned structure.
  • Field based + HQ Montecarlo
    This option performs a Montecarlo optimization like in the Field based + Montecarlo option but with a more accurate similarity assessment. This option is not intended for large libraries since it is significantly slower.
Similarity index

The Similarity index section enables to select which similarity metric should be used to compare molecules. By default, the Tanimoto coefficient is used but also the Tversky index can be selected.

Manual setup of Fields and Weights

The Manual setup of Fields and Weights enables to configure which fields should be used to compare molecules and which weight should each weight have in the overall similarity. In order to configure them you need switch on the Manual setup of Fields and Weights button and configure the fields and their weights. You may set a total of three fields. For each field, you can select different options: Electrostatic, Shape, Hydro Total, Hydro Electrostatic, Hydro Cavitation, Hydro Van Der Waals, and HBond Acceptors/Donors. Finally, for each of the selected fields, you need to assign a percentage of weight (note that the rate needs to sum 100).

Number of threads

This option is used to select the number of threads used in the execution of the Virtual Screening Node.

Log file name

This option is used to indicate the path of the output log file.

SSH Configuration

Remote execution

Host

Address of the host.

Port

Port of the service.

Authentication

Method of authentication.

  • Password
    Use username and password to authenticate.
  • Keyfile
    Use keyfile to authenticate.
User

Name of the user.

Password

Password of the user, if authentication via password is selected.

Keyfile

Location of the keyfile. Note that the key file has to be in OpenSSH key file format.

Timeout

Specify the timeout for the connection in milliseconds here.

Test connection

Open dialog that test the current connection.

Input Ports

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The molecule library to be screened.The way of selecting files is the same as for the input file described in the file preparation options and the preferred file type is SDF. It is also recommended to use a file with conformations generated for each molecule in order to take into account molecular flexibility.
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The reference molecules to do the screening In this sport, you should select a file with all the molecules with known activity that you want to use. Crystal structures are preferred in case they are available and the file should not include many of them as simulation times will be increased significantly. The way of selecting files is the same as for the input file described in the file preparation options and the preferred file type is SDF.

Output Ports

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Table with the output molecules.
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Table with the PharmScreen csv file ranking.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install Pharmacelera Extensions from the following update site:

KNIME 4.3

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Developers

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