Explore
Discussed in group meeting today.
Maybe explore MCS (Maximum Common Substructure) to establish a tress of the LOTUS structural set.
Some refs
https://www.mdpi.com/2079-3197/8/2/48
https://pubs.acs.org/doi/full/10.1021/acs.jcim.0c00741
https://chemistry-europe.onlinelibrary.wiley.com/doi/full/10.1002/cmdc.201700482
Very likely Luca should have some ideas on this and this is a subgraph search problemeatic.
Would offer the advantage over and complement classical chemical classifiers as we would have a chemical structures associated with higher taxonomomical levels.
rBAN: retro-biosynthetic analysis of nonribosomal peptides https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0335-XXXX
In silico methods for linking genes and secondary metabolites: The way forward https://www.sciencedirect.com/science/article/pii/S2405805X1530020X
Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP https://www.nature.com/articles/s41467-022-30970-9
http://biopathnavi.qmclab.com/ https://github.com/prokia/BioNavi-NP
https://retrorules.org/ https://retrorules.org/diy
Enumerating all possible biosynthetic pathways in metabolic networks https://www.nature.com/articles/s41598-018-28007-7
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives https://www.nature.com/articles/s41467-021-22022-5
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx https://www.nature.com/articles/s41467-022-29238-z#MOESM1
Exploring Chemical Biosynthetic Design Space with Transform-MinER https://doi.org/10.1021/acssynbio.9b00105
A pathway for every product? Tools to discover and design plant metabolism https://doi.org/10.1016/j.plantsci.2018.03.025
Efficient Enumeration of Branched Novel Biochemical Pathways Using a Probabilistic Technique https://doi.org/10.1021/acs.iecr.1c02211