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Phase Hypothesis Identification

DeprecatedDeprecated Nodes version by Schrödinger

This node is deprecated. Please use "Phase Hypothesis" mode in "KNIME-Maestro Connector" to identify Hypothesis in Maestro and send them back to KNIME.

The Phase hypothesis identification node runs sequentially pharmacophore site creation, common pharmacophore perception and hypothesis scoring.

A set of pharmacophore feature definitions is applied to each ligand conformation to identify the positions of all pharmacophoric elements in that ligand.

During common pharmacophores identification all n-point pharmacophores from the input ligands are enumerated and filtered into a set of high-dimensional boxes. Pharmacophores that fall into the same box are similar enough to be considered equivalent. Boxes that receive at least one pharmacophore from a sufficient number of actives are said to "survive" the partitioning process. Each surviving box may be processed in the subsequent Score Actives step to identify a pharmacophore hypothesis from that box. Hypotheses are scored with respect to input ligands by assigning numerical rankings to the pharmacophores within each surviving box. The highest scoring pharmacophore in a given box is designated as a hypothesis, and the ligand giving rise to that pharmacophore is known as its reference ligand. The scoring function considers the quality of the alignments, of the oriented feature overlay and of the conformation volume overlap.

Backend implementation

These command line tools pharm_project, pharm_create_sites, pharm_find_common, phase_partition, pharm_score_actives, and phase_scoring are used in sequence to implement this node.


Column containing input
Select the column in the input data table that contains the input conformers.
Pharmacophore feature definitions file
Use the specified pharmacophore feature definitions. If omitted, the default definitions from the Phase installation will be used.
Number of sites
The number of sites in each common pharmacophore. Must lie between 3 and 7.
Must match at least N active ligands
The minimum number of ligands that must match a pharmacophore before it can be considered common. Must lie between 2 and the number of input ligands.

Input Ports

Conformers of known active compounds in Maestro format

Output Ports

Score Actives Data and Hypotheses


Std output/error of Phase Hypothesis Identification
Std output/error of Phase Hypothesis Identification
create_sites Log output
create_sites Log output
find_common_partition Log output
find_common_partition Log output
score_actives_scoring Log output
score_actives_scoring Log output

Best Friends (Incoming)

Best Friends (Outgoing)


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