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SiteMap

Schrödinger extension for KNIME Workbench version 20.3.139.202008121324 by Schrödinger

Carries out a site-finding job, then calculates SiteMaps for each qualifying site-point grouping, and finally evaluates the SiteMap results and summarizes the characteristics of the sites in a series of Maestro properties.

Backend implementation

$SCHRODINGER/sitemap

Options

Column containing input structures
Select column in the data input table containing the structures
Requires at least N site points per reported site
Minimum number of site points needed to report a site grouping (default, 15)
Report up to N sites (site-point groupings)
Find/report up to this number of sites (default, 5)
Definition of hydrophobicity to use
Set definition to be used in defining hydrophobic regions (default, 3)
(more restrictive=3, less restrictive=0)
Grid size to use
Grid size to be used in the SiteMap calculations (default, 0.7 A)
("coarse"=1.0 A, "standard"=0.7 A and "fine"=0.35 A)
Crop site maps at N angstroms from nearest site point
Restrict displayed SiteMaps to N angstroms from the nearest site point (default, 4 A).
Force field to use
Version of OPLS to use (default, OPLS_2005)
Keep log files
Keeps the log files from all the stages(default is "no")
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: SiteMap
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 from command line, just specify the option_name and the value as _off_ through the flow variable.

To pick the value from a column in the input table, specify the option_name and the value as :column_name: through the flow variable. Any column other than String, Integer and Double types will be written to a file and the file name is added as the option value.
Note: To use the "Evaluate a single binding site region" mode, the following flow variables have to be defined: SiteMap-ligmae and SiteMap-sitebox.

Input Ports

Icon
Prepared protein structures in Maestro format

Output Ports

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Sites in Maestro format

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.2
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Developers

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