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Shape Screening

DeprecatedDeprecated Nodes version 21.1.156.202102141445 by Schrödinger

Screens a list of molecules against a shape query. Each conformer from a given molecule is aligned to the query in various ways, and a similarity is computed based on overlapping hard sphere volumes. The conformer and alignment yielding the highest similarity for each molecule is written to the output, along with the similarity property r_phase_Shape_Sim, which appears in the Project Table as "Shape Sim".

Backend implementation

$SCHRODINGER/shape_screen

Options

Column containing shape input
Select the column containing the shape query (either Maestro or SD type)
Column containing ligand input
Select the column containing structures to be screened (either Maestro or SD type)
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

Atom types to use for volume scoring
Consider atom types when computing similarities. If this option is used, overlapping volumes will be computed only between atoms of the same type, so that alignments will favor superposition of chemically similar atoms. The supported atom typing schemes are:

1. MacroModel - MacroModel atom types.

2. Element - Elemental types.

3. Pharmacophore - Generalized pharmacophoric types: D - H-bond donor hydrogen, H - hydrophobic/non-polar, N - negative ionic, P - positive ionic, W - electron-withdrawing, X - other

Generate conformers
Generate conformers on-the-fly.
Maximum number of conformers
Maximum number of on-the-fly conformers.
Retain up to v conformers per rotatable bond
Number of on-the-fly conformers to retain per rotatable bond in the structure. The total number of conformers is bounded by the product of v and the number of rotatable bonds. Note that if the maximum number of conformers is increased, v may have to be increased as well in order to retain additional conformers for more rigid structures.
Conformational energy window (kcal/mol)
On-the-fly conformational energy window in kcal/mol.
Amide bonds
On-the-fly amide torsion sampling.
Search methods
On-the-fly search method.
Maximum number of alignments to report #
Report up to # aligned structures for each screening molecule, grouped and sorted by decreasing similarity.
Score in place
Compute similarities without aligning.
Filter out conformers with similarity below (0-1)
Filter out molecules whose similarities fall below this value
Include polar hydrogens
Consider hydrogens attached to non-carbon atoms when computing shape similarity. By default, all hydrogens are ignored.
Maximum Number of Processors
Maximum number of processors to use on selected host - only used if 'Generate conformers' option is selected.
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: ShapeScreen
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.

Input Ports

Icon
The shape query (in Maestro or Sd Format)
Icon
Structures to screen (in Maestro or Sd Format)

Output Ports

Icon
Screening results

Views

Log output of Phase Shape
Log output of Phase Shape

Installation

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

KNIME 4.3

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Developers

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