The virtual screening module enables you to perform a virtual screening campaigns using different alignment (including 3D molecular field alignment) and similarity methods. More advanced options are available to customize the scoring function.
Platform compatibility: On Windos and Mac, it is necessary to have Pharmacelera-API running. On Linux, it can work with or without API running (different options will appear if API is running or not).
Select the column from previous node that contains the path to the file.
Select the column from previous node that contains the path to the file.
IP address where the Pharmacelera API is running. Default is http://localhost (local execution).
Port to access Pharmacelera API (Default 8080).
Use this option to indicate the path to 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).
skip: This option disables molecular alignment. It can be selected to use user-provided alignments (e.g. using alignments from a docking).
structure: A substructure alignment is performed maximizing field similarity.
field: Molecule alignment is performed maximizing field similarity using the molecular moments of the selected fields of interaction.
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.
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.
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.
Select tanimoto or tversky
Working directory where screening files are stored. You can enter Windows, Linux or macOS paths.
When using API, a folder name output will be created. All API executions will be saved there with the output name given.
Windows: C:/PATH/TO/WORKDIR
Linux/MacOS: /PATH/TO/WORKDIR
Name of the folder that contains the outputs of the node.
When using API, a folder name output will be created. All API executions will be saved there with the output name given.
This option is used to select which field of interaction is going to be used to align and compare molecules. Up to three fields can be used in parallel to build the final similarity score. By default, PharmScreen is configured to use the Electrostatic (hydroele) and Cavitational (hydrocav) contributions to hydrophobicity and the H-Bond Acceptors/Donors (hbond) fields.
Default: Hydroele
This option is used to select the importance that each of the three available fields have in the overall similarity score. The sum of the three weights must be 1. By default, PharmScreen is configured to use the Electrostatic (0.25) and Cavitational (0.65) contributions to hydrophobicity and the H-Bond Acceptors/Donors (0.1) fields.
Default value: 0.25
Default: Hydrocav
Default value: 0.65
Default: Hbond
Default value: 0.10
Enter any option using command line format. For example:
--sanitize --threads 8
Only if you are running Knime on Linux and you want to use the executable of PharmScreen installed locally in your drive.
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To use this node in KNIME, install the extension Pharmacelera extensions from the below update site following our NodePit Product and Node Installation Guide:
A zipped version of the software site can be downloaded here.
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