from fragmenstein.laboratory.validator import hits_check
Fragmenstein
Stitched molecules
Fragmenstein: Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse.
Fragmenstein can perform two different tasks:
Combine hits (merging and linking) based on their atomic overlap
Place a given followup molecule based on one or more parent hits
NB. Whereas docking uses pre-generates comformers and finds the best pose that best matches the parent (if set-up to do so), Fragmenstein creates a monstrous comformer from the parent(s) and then minimises it, optionally in the protein. Hence why I call it a ‘placement’ not docking tool.
Index
For documentation in Read-the-documents see fragmenstein.readthedocs.io. For GitHub documentation see:
Python usage — ideal for coders!
Command line usage — ideal for non-coders!
Badges and notebooks
Example of multiple applications: .. image:: https://img.shields.io/youtube/views/kieDWYkzmiE
- target:
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See Also
ChemRXiv preprint — https://chemrxiv.org/engage/chemrxiv/article-details/65d751ab9138d23161b7ea38
Fragmenstein is used in Schuller et. al. 2021
Figures for the upcoming manuscript are in a separate repo
The conversion of a rdkit Chem.Mol that cannot be sanitised to an analogue that can is done by the molecular rectifier package
The conversion of a rdkit Chem.Mol to a PyRosetta residue type (a “params file”) is done via the rdkit-to-params package
The pipeline demo colab notebook uses Brian Shoichet’s SmallWorld webapp, interfaced via its API in Python
The playground demo colab notebook features a JSME widget — JSME is a popular JS only molecular editor
Molecular Rectifier is used to correct the mistakes in the merged molecules, and is usable for other algorithms, especially de novo design via denoising diffusion probabilistic models (cf blogpost discussion for the latter)
Fragmenstein combine route does not check if a compound is purchasable. Above NextMove Software SmallWorld is used (SmallWorld hosted by John Irwin) to find the top N analogues, via an API.
In Arthorian Quest, a parent combound is coverted with ease into an ambiguous SMARTS pattern, catalogue compounds are searched with NextMove Software’s Arthor (hosted by John Irwin) and then placed with Fragmenstein.
Steph Wills’s fragment network merges repo enumerates superstructures of two parent hits from catalogue and places them with Fragmenstein.
SynDirElla performs a retrosynthesis of a compound, enumerates close analogues of the synthons and places their combinations
