CATEGORY
Molecular Screening
SOURCE
RDKit
DESCRIPTION
Performs 3D alignment of molecules using Open3DAlign
INPUTS
- input: a dataset of molecules to be aligned
- queryMol: a data containing the query 3D structure
OUTPUTS
A dataset of molecules
OPTIONS
| Query mol index | The index of the structure in the queryMol dataset. Default is the first. |
| O3DAlign score threshold | Alignment score threshold determining which structures are output. If not specified then all are output. |
| Number of conformers | Number of conformers to generate (leave empty if input already contains 3D structures). |
| Use Crippen (logP) contributions | Include Crippen (logP) calculations in the alignment. |
ADDITIONAL INFO
Open3DAlign can be used to perform a rigid alignment of 3D structures. Details can be found here. It has been incorporated into RDKit, which is how it is used by this cell.
The input to the cell can either already contains 3D conformers or they can be generated by the cell. If you want them to be generated specify a positive value for the Number of conformers option.
The input to the cell can either already contains 3D conformers or they can be generated by the cell. If you want them to be generated specify a positive value for the Number of conformers option.
The output are the structures aligned to the query molecule. The target molecule is translated and rotated to optimise the alignment, but the internal geometry is unmodified.
The alignment scores that are generated are only valid for that particular query molecule. They are numbers, typically in the range of 50 - 150 (bigger scores mean better alignments). The “ideal” score can be determined by aligning the query to itself (let’s call this score Q). You can control which structures are output using the O3DAlign score threshold option (let’s call this T) which allows target structures that have an alignment score lower than Q - T to be excluded from the output. You may need to play with this option to get the desired output.