Phase Screening

Screens one or more pharmacophore hypotheses against one or more structure files or Phase databases.

Backend implementation

Options

Column containing hypotheses

Select the column containing pharmacophore hypotheses

Column containing matches

Select the integer column containing minimum number of hypothesis sites to match. Selecting '-- All sites --' will match all sites and selecting '-- 4 sites --' will match 4 sites

Screen structures in

Select the Screen source from three options: File, Input Structures or Phase Database

Column containing structures to screen

Select the column containing structures to be screened (either Maestro or SD type). Enabled only if "Input Structures" is selected.

File name

Browse to a structure file or Phase Database. Enabled only if File or Phase Database is selected.

Output Column Structure

Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Include log in output

Include Log column in output table. If output type is Sdf, Log column can't be added to output

Settings...

On clicking "Settings" button, this node brings up the "Phase Ligand Screening" Python panel for configuration.

Parameter flow variables

Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: PhaseScreen
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option without a value, specify the option_name and the value as _off_ through the flow variable.

To remove an existing option with a value, specify the option_name and the value as _rm_ through the flow variable.

Views

Stdout/error of Phase Screen

Stdout/error of Phase Screen

Workflows

• Ligand alignment with a pharmacophoreKNIME Hub
• Pharmacophore screening - from the KNIME hubKNIME Hub
• Pharmacophore screening - ready to be deployed to LiveDesignKNIME Hub
• Pharmacophore screening - to be prepared to be run in LiveDesignKNIME Hub
• Phase screeningKNIME Hub
• Phase screening 1KNIME Hub
• Phase screening 1-2KNIME Hub
• Phase screening 1-3KNIME Hub

Links

• No links available

Developers