Metabolic circuits are a promising alternative to other conventional genetic circuits as modular parts implementing functionalities required for synthetic biology applications. To date, metabolic design has been mainly focused on production circuits. Emergent applications such as smart therapeutics, however, require…
We present an algorithm to compute molecular graph descriptors considering the stereochemistry of the molecular structure based on our previously introduced signature molecular descriptor. The algorithm can generate two types of descriptors, one which is compliant with the Cahn-Ingold-Prelog priority…
De novo biosynthetic pathways are designed, assembled and optimized to produce high-value compounds such as drugs and chemical building blocks from renewable resources. Microorganisms are used as synthetic platforms of systems biology where biochemical pathways are engineered into the host…
When considering the best metabolic pathways to engineer into a chassis organism in order to synthesize heterologous target compounds, the problem of enumerating all possible heterologous pathways linking a target compounds to a source set of compounds needs to be…
How enzymes have evolved to their present form is linked to the question of how pathways emerged and evolved into extant metabolic networks. To investigate this mechanism, we have explored the chemical diversity present in a largely unbiased dataset of…
Synthetic biology and metabolic engineering are used to develop new strategies for producing valuable compounds ranging from therapeutics to biofuels in engineered microorganisms. When developing methods for high-titer production cells, toxicity is an important element to consider. Indeed the production…
Synthetic biology is used to develop cell factories for production of chemicals by constructively importing heterologous pathways into industrial microorganisms. In this work we present a retrosynthetic approach to the production of therapeutics with the goal of developing an in…
Unlike in the related area of bioinformatics, few books currently exist that document the techniques, tools, and algorithms of chemoinformatics. Bringing together worldwide experts in the field, the Handbook of Chemoinformatics Algorithms provides an overview of the most common chemoinformatics…
Chemical compound space (CCS) is the combinatorial set which encompasses all chemical compounds. It can be viewed as the high dimensional space spanned by all the possible stoichiometries and configurations of electrons and atomic nuclei which form molecular or condensed…