Screen3D

Screen3D is a search tool that offers a new and fast similarity search strategy for three dimensional molecular structures. It helps the top ranking of molecules regarding their 3D structures.

Options

Query structure column
The query structure column.
Target structure column
The target structure column.
Screen method
  • Shape: scores full molecular shape similarity. The result of this algorithm derives from the van der Waals volume overlap of molecular pairs.
  • Match: similarity score is based on calculating the atomic distances within the query and target molecules respectively. Atom type, 3D geometry and conformational flexibility are incorporated in this method.
Alignment types
  • Align by extended atom types: extended atom types are assigned to each atom to enable chemically relevant atomic overlay. During the alignment process the overlap of the atoms of the same type is maximized. Types differentiate atomic number, hybridization state and aromaticity, e.g. aromatic nitrogen atom is not matched against a tertiary amine. These extended atom types correspond to the ones used in Dreiding force field.
  • Align by pharmacophore types: atoms are overlaid by their pharmacophoric properties: positive, negative, aromatic, hydrophobic, H bond donor and acceptor. Directionality is also taken into account at the H bonds. Atoms of the same types are attempted to align.
  • Align by common scaffold (MCS): the atom-atom pairing is obtained from the 2D maximum common substructure of the molecules. Alignment by extended atom types is applied on the non MCS atoms.
Minimum flexible ring size
Rings are treated flexible in case their size (number of atoms) exceeds this limit.
Minimum number of non-barred bonds in flexible rings
Rings are treated flexible in case their non barred bond count exceeds this limit. Barred bonds are aromatic, amide, double, a member of another ring that is not flexible and a single bond that connects two aromatic rings.
Common scaffold minimum size
Only available at MCS based alignment. Minimum number of atoms that are required for the maximum common substructure calculation prior to the alignment.
Accuracy
low, normal, high, very high: If lower selected the calculation is faster. The default is normal.

Input Ports

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Input table that contains query structure in Structure(Mrv, Sdf, Smiles, etc.) format.
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Input table that contains target structure in Structure(Mrv, Sdf, Smiles, etc.) format.

Output Ports

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Output table that contains three dimensional similarity value.

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Installation

To use this node in KNIME, install the extension ChemAxon/Infocom JChem Extensions Feature from the below update site following our NodePit Product and Node Installation Guide:

v5.9

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

Plugin provider: Infocom Corporation
Plugin version: 4.7.0.v250304
On NodePit since: 2025-12-17
Last update: 2026-01-07
KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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