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- RDkit (http://www.rdkit.org/)
- pandas (https://pandas.pydata.org/)
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- GAMS (https://www.gams.com/)
- CPLEX solver
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Description:
- rePrime
- rePrime procedure identifies and captures as a reaction rule the molecular graph topological changes underpinning the substrate to product graph conversion.
- novoStoic
- An MILP procedure to identifies a mass-balanced de novo biochemical network that converts a source metabolite to a target while satisfying a multitude of constraints and optimizing the objective function.
- How to cite rePrime/novoStoic -"Kumar, Akhil, et al. "Pathway design using de novo steps through uncharted biochemical spaces." Nature communications 9.1 (2018): 184."
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