IconCombiGlide Library Enumeration0 ×

Schrödinger Nodes for Suite2018-1 version 0.0.1.7B27VcMf4_L7A58S5A8G55JS by Schrödinger

The combinatorial library enumeration is carried out by substitution of attachments on the core structure with fragments from the reagent structures. For both the core and the reagents, the bonds to be broken must be designated before-hand. The fragments from the reagents are then attached to the core at the site of the broken bond. This process can be regarded as "growing" the new attachment onto the core in place of the old attachment, and the bond that is replaced (with its attached atoms) is called the grow bond. These bonds are not necessarily the bonds that are broken and formed in the real chemical reaction, but represent a means of varying the attachments to a core structure that might include part of the real reagent. To generate a combinatorial library, you must have a core structure whose attachments you want to replace are defined by setting the s_m_grow_name property of the first atom that defines the attachment bond to '1f' and the second atom to to '1t'. This can be done by either manually editing the core structure file or within Maestro. The second attachment point would be labeled with '2f' and '2t' and so on. For each attachment point, a set of reagent files that define the replacements must be prepared individually using the CombiGen Reagent Preparation node.

Backend implementation

$SCHRODINGER/combgen

Options

Column containing core structure
Column in input table containing the core structure containing attachment point information
Note:
The core input can be generated as below:
1. Load the structure to be used as core in Maestro
2. In Applications => CombiGlide => "Combinatorial Library Enumeration..." wizard, pick the molecule, then define the attachment points (specifying a mock-up bld file) and start the calculation.
3. The calculated input Maestro file can be read in with a "Molecule Reader" node.
Or
The Run Maestro 1:1 Metanode can be used to define the attachments. See the workflow example (https://www.schrodinger.com/knimeworkflows/#Library_Design).
Column containing prepared reagents
Column in input table containing the reagents prepared using the CombiGlide Reagent Preparation Node. Regents of the same type should be grouped and ordered in the same way as the associated attachment points in the core structure. So for example the first group of structures in the input table consist of amines and will be used with the first attachment point in the core structure. The second group of alcohols will be used with the second attachment point, etc.

Input Ports

Input data table containing the core structure in Maestro format
Input data table containing reagent molecules in Maestro format

Output Ports

Output data table containing combinatorial library molecules in Maestro format

Views

Log output of CombiGlide Library Enumeration
Log output of CombiGlide Library Enumeration

Workflows

Update Site

To use this node in KNIME, install Schrödinger Nodes for Suite2018-1 from the following update site:

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