List of computer-assisted organic synthesis software explained

Computer-assisted organic synthesis software is a type of application software used in organic chemistry in tandem with computational chemistry to help facilitate the tasks of designing, predicting, and producing chemical reactions. CAOS aims to identify a series of chemical reactions which, from a starting compound, can produce a desired molecule. CAOS algorithms typically use two databases: a first one of known chemical reactions and a second one of known starting materials (i.e., typically molecules available commercially). Desirable synthetic plans cost less, have high yield, and avoid using hazardous reactions and intermediates. Typically cast as a planning problem, significant progress has been made in CAOS.

CAOS programs

• Spaya - Retrosynthesis planning tool freely accessible provided by Iktos
• IBM Rxn - https://rxn.res.ibm.com/
• AiZynthFinder - A freely accessible open source retrosynthetic planning tool developed as a collaboration between AstraZeneca and the University of Bern. AiZynthFinder predicts synthetic routes to a given target compound, and can be retrained on a users own dataset whether from public or proprietary sources.^{[1] [2] [3]}
• Manifold - Compound searching and retrosynthesis planning tool freely accessible to academic users, developed by PostEra
• WODCA – no trial version; proprietary software^[4]
• Organic Synthesis Exploration Tool (OSET) – open-source software, abandoned^[5]
• CHIRON – no trial version; proprietary software^[6]
• SynGen – demo version; proprietary software; a unique program for automatic organic synthesis generation; focuses on generating the shortest, lowest cost synthetic routes for a given target organic compound, and is thus a useful tool for synthesis planning
• LHASA – demo available but not linked (?); proprietary software
• SYLVIA – demo version; proprietary software; rapidly evaluates the ease of synthesis of organic compounds; can prioritize thousands of structures (e.g., generated by de novo design experiments or retrieved from large virtual compound libraries) according to their synthetic complexity^[7]
• ChemPlanner (formerly ARChem – Route Designer) - is an expert system to help chemists design viable synthetic routes for their target molecules; the knowledge base of reaction rules is algorithmically derived from reaction databases, and commercially available starting materials are used as termination points for the retrosynthetic search
• ICSYNTH – demo available; proprietary software; A computer aided synthesis design tool that enables chemists to generate synthetic pathways for a target molecule, and a multistep interactive synthesis tree; at its core is an algorithmic chemical knowledge base of transform libraries that are automatically generated from reaction databases.^[8]
• Chematica (Now known as Synthia)
• ASKCOS – Open-source suite of synthesis planning and computational chemistry tools.^[9]

See also

• Comparison of software for molecular mechanics modeling
• Molecular design software
• Molecule editor
• Molecular modeling on GPU
• List of software for nanostructures modeling
• Semi-empirical quantum chemistry methods
• Computational chemical methods in solid state physics, with periodic boundary conditions
• Valence bond programs

Notes and References

1. https://github.com/MolecularAI/aizynthfinder AiZynthFinder GitHub
2. https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00472-1 AiZynthFinder Paper
3. https://pubs.rsc.org/en/content/articlelanding/2020/SC/C9SC04944D AiZynthFinder: datasets and their performance in the pharmaceutical domain paper
4. http://www2.chemie.uni-erlangen.de/software/wodca/ WODCA
5. http://www.sai.msu.su/sal/Z/2/OSET.html OSET
6. Web site: CHIRON . 2013-02-18 . https://web.archive.org/web/20150416001829/http://osiris.corg.umontreal.ca/chiron.shtml . 2015-04-16 . dead .
7. http://www.molecular-networks.com/products/sylvia SYLVIA
8. https://www.deepmatter.io/products/icsynth/ ICSYNTH
9. https://askcos.mit.edu/