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Pharmacophore Screening

DeprecatedDeprecated Nodes version 21.1.156.202102141445 by Schrödinger

Launches a job that searches a set of Maestro structures for matches to a pharmacophore hypothesis. This node iterates through all combinations of hypothesis files, minimum sites to match, and intersite distance matching tolerance.

Backend implementation

$SCHRODINGER/phase_screen

Options

Column containing hypothesis input
Select column in the data input table containing the hypotheses
Column containing structures
Select column in the data input table containing the input Maestro structures
Include Log in Output
If selected, a log column will be added to the output table
Source of conformations
Specify whether to use existing conformations or to generate them during the search.
Score in place
Score structures without doing any alignment to the hypothesis
Limit CPU time for matching to N seconds/molecule
Select this option and enter a time in the text box to restrict the amount of CPU time used per molecule in the search. Limiting the CPU time is useful when doing partial matching for hypotheses with many sites, as the time spent finding matches to a given molecule may become very large because of combinatorial considerations.
Distance matching tolerance
A list of values is specified. This node iterates through all combinations of hypothesis files, minimum sites to match, and intersite distance matching tolerance.
Minimum number of hypothesis sites to match
A list of values is specified. This node iterates through all combinations of hypothesis files, minimum sites to match, and intersite distance matching tolerance. If "Prefer partial matches involving more sites" is checked, then only the first number of hypothesis sites to match is used, all the rested are grayed out and not used. Not used if the searching method is fetch.
Prefer partial matches involving more sites
If this option is selected, matches involving fewer than n sites will not be sought if there are any matches with n sites
Consider atom types when computing volume scores
Option for computing volume scores using overlap only between atoms of the same MacroModel atom type. This option favors alignments that superimpose chemically similar atoms.
Apply site mask to partial matches
Flag for applying a site mask to partial matches. The default is true if hypoID.mask exists and false if not.
Apply feature-matching rules
Flag for applying feature-matching rules, which associate permitted and prohibited features with each site in the hypothesis. The default is true if hypoID.rules exists and false if not. Note that if the feature rules permit any site to be matched to more than one type of feature, vector scoring will be turned off.
Apply feature-based matching tolerances
Flag for applying feature-specific matching tolerances. The default is true if hypoID.tol exists and false if not.
Apply hypothesis-specific matching tolerances
Flag for applying hypothesis-specific matching tolerances. The default is true if hypoID.dxyz exists and false if not.
Use QSAR model
Flag for applying a QSAR model to hits. The default is true if hypoID.qsar exists and false if not.
Apply excluded volumes
Flag for applying excluded volumes to hits. The default is true if hypoID.xvol or hypoID.ev exists and false if not. If both files exist, hypoID.ev is used.
Return at most
Limit the number of hits listed per molecule - some molecules can return more than one hit because different alignments or different conformers might match the hypothesis.
Fitness score weights
Specify the weights of the alignment score, the vector score and the volume score, and set the threshold for distance matching.
Reject hits with
These three options allow you to reject hits that do not meet the specified cutoff for the given scores. The alignment score cutoff cannot be edited; the other two score cutoffs (vector and volume) can be changed

Input Ports

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Hypotheses input
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Molecules in Maestro format

Output Ports

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Molecules in Maestro format that match the pharmacophore hypothesis. This is a result of all of the executions from the combinations of hypothesis files, minimum sites to match, and intersite distance matching tolerance specified. The output could have multiple CTs in each cell: to split them up, use the MAE Expander node.

Views

Std out/err of Find Matches in Phase Screening
Std out/err of Find Matches in Phase Screening

Best Friends (Incoming)

Best Friends (Outgoing)

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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