Activity Profiling

The Activity Profiling node screens ldb databases against multiple LigandScout pharmacophores.

Options

Settings

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)

Check exclusion volumes

Enables the consideration of exclusion volumes during the screening process.
(Default: enabled)

Include non-matching molecules

If this option is set, the output table and the output view will also include molecules that did not match any of the input pharmacophores. Should only be used with small input compound databases.
(Default: disabled)

Include non-matching pharmacophores

If this option is set, the output table and the output view will also include pharmacophores that were not matched by any input molecules.
(Default: disabled)

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.

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.

Download Remote Default Settings

Pressing this button will download server-side defaults for the below described job submission settings.

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.

Views

Heat map

This view displays the results in a heat map. Different colors indicate how likely a specific interaction is.

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