Epik Classic

Epik is a program for the prediction of the pKa values of the ionizable groups in ligands, and for the generation of the probable ionized and tautomerized structures within a given pH range. Epik rapidly and consistently predicts pKa values, employing the widely used and respected Hammett and Taft empirical equations. The values of the parameters in these equations are determined from fits to experimental data either from the literature or from Schrödinger's own development efforts. Tautomer probabilities are estimated using a database of tautomerizations derived from experiment and quantum chemical calculations. Both the ionization and tautomerization employ user-modifiable databases of parameters. Collections of probable structures are generated by iteratively tautomerizing and ionizing the base structure.

For additional documentation on the available options see the Epik documentation.

Note that the predicted pKa values are added as additional Maestro properties to the output structures.

Backend implementation

$SCHRODINGER/epik

Options

Column containing input

Choose the input column for the external program

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

Match Input

Epik generates a molecule (or list of molecules) for each input molecule. Since each Maestro type cell can either hold one or more CTs, this option determines whether each output cell includes the same number of cells as the input, with potentially multiple CTs (if selected) or one CT per cell (unselected). If the Match Input is not selected, and the output columns have input columns, then the matching input row data is duplicated for each output molecule.

Input Ports

: Molecules in Maestro format

Output Ports

: Molecules in Maestro format (with additional properties)

Popular Predecessors

Popular Successors

Views

Log output of Epik: Log output of Epik

Workflows

Developers

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Installation

To use this node in KNIME, install the extension Schrödinger Extensions for KNIME from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Schrödinger

Plugin version: 24.1.135.v202402072122

On NodePit since: 2023-12-06

Last update: 2024-04-19

KNIME versions: v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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