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IScreen

LigandScout Extensions for the KNIME Workbench version 1.7.9 by InteLigand GmbH

The IScreen node screens ldb databases against LigandScout pharmacophores.

Options

Settings

Scoring function
Choose the scoring function type that validates the alignments. The Pharmacophore-Fit scoring function only considers pharmacophoric features and the feature RMSD. The Relative Pharmacophore-Fit scores the number of matching pharmacophore features and the RMSD of the pharmacophore alignment normalized to [0..1].
(Default: Pharmacophore-Fit)
Screening mode
In Match all query features mode the database is browsed to find molecules that are fully matching the given set of query pharmacophores. Whereas in Fragment screening mode, the database molecules are fitted into the query pharmacophores. In the latter case, the query is partially matched.
(Default: Match all query features)
Retrieval mode
Stopping criteria per compound. Stop after first matching conformation: the screening for a molecule stops when the first matched conformation is found. Get best matching conformation: all conformations are examined for the best matching conformation. Get all matching conformation: all conformations that match the query pharmacophore are shown as screening hits. The last two modes could slow down screening.
(Default: Stop after first matching conformation)
Max. num. of omitted features
Defines the maximum number of query features that can be omitted during the Match all query features mode. If zero is specified, the whole query pharmacophore must be matched to be a valid hit.
(Default: 0)
Min. num. of required features
Specifies the minimum number of required features that has to match between the library molecule and the query pharmacophore to be a valid hit. This setting is only enabled if the Fragment screening mode is chosen.
(Default: 3)
Boolean expression
The node provides the functionality to combine pharmacophores using boolean expressions ( “AND” / “OR”). For instance: “(3 AND 2) OR 1” means that a valid hit needs to be matched to pharmacophore 3 and 2, or only to pharmacophore 1.
(Default: empty, which is equivalent to '1 OR 2 OR 3 OR...')
Check exclusion volumes
Enables the consideration of exclusion volumes during the screening process.
(Default: enabled)
Use remote cluster
Remote execution enables the fast screening of large compound databases and the efficient usage of multiple target models at once. Behind the scenes, the LigandScout Remote Execution feature sends the input pharmacophore model(s) to the remote cluster where the screening job is executed.
Terminate on cancel
If selected, the node will terminate the remote job when it is canceled. Please note that nodes are automatically canceled when the KNIME workbench is closed. Alternatively, jobs can be managed via the Remote Screening Monitor node.
(Default: disabled)
Job name
Specifies the name of the new remote job than can later be used to distinguish between jobs.
Split database files using chunk size
Allows to split remote screening jobs not only per physical database chunk but additionally by using a specific amount of molecules. If enabled, one physical database chunk file might be screened using several scheduler sub-job executions.
Decrease priority by
Can be used to decrease the priority of the new jobs in the scheduling queue. A higher value means that the job should have less priority.
Processors per sub-job
Sets the number of processors used by each sub-job.
IScreen #cores
Specifies the maximum amount of threads used by one sub-job.
IScreen memory (in GB)
Specififes the maximum amount of memory used by one sub-job.

LigandScout Server

Overview
The LigandScout Server Settings are required for establishing a connection to a LigandScout Server instance used for remote execution on High Performance Computing clusters. See chapter Remote Execution for more details on these features.
IP or hostname
Sets the IP or hostname of the cluster machine that the LigandScout Server is running on.
Port
Sets the port that the LigandScout Server is listening on.
(Default: 8080)
SSH Port
Sets the port used for the SSH protocol on the server host.
(Default: 22)
User
This field should be set to your username on the remote cluster.
Identity File
Sets the path to the secret key file used to authenticate with the remote cluster.
Use Password
If selected, a password can be used instead of the secret key file. Please beware that the password has to be stored on this computer. It is therefore recommended to use an identity file.
Use intermediate Host
If selected, the below settings will be enabled. Usage of an intermediate host allows to tunnel the connection through another host and this way reach otherwise inaccessible clusters. This can be necessary if a firewall restricts access from outside your organizational network or if a gateway host is required to access the remote cluster.
IP or hostname
Sets the IP or hostname of the intermediate host that has access to the remote cluster.
SSH Port
Sets the port used for the SSH protocol on the intermediate host.
(Default: 22)
User
This field should be set to your username on the intermediate host.
Identity File
Sets the path to the secret key file used to authenticate with the intermediate host.
Use Password
If selected, a password can be used instead of the secret key file. Similar to above, please beware that the password has to be stored on this computer. It is therefore recommended to use an identity file.

Input Ports

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Table containing the file references to the input databases
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Table containing the pharmacophore(s) for the query-set

Output Ports

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Table containing the hits retrieved from the screening

Views

ROC Curve
The view shows a ROC Curve created using the active and decoy database flags of the input databases.

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

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

KNIME 4.3

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Developers

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