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Article
Open AccessEzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions
Over the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on biological catalysis is now ripe for use as the foundation of new kno...
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Article
Open AccessUsing mechanism similarity to understand enzyme evolution
Enzyme reactions take place in the active site through a series of catalytic steps, which are collectively termed the enzyme mechanism. The catalytic step is thereby the individual unit to consider for the pur...
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Protocol
Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function
The goal of our research is to increase our understanding of how biology works at the molecular level, with a particular focus on how enzymes evolve their functions through adaptations to generate new specific...
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Article
WhichP450: a multi-class categorical model to predict the major metabolising CYP450 isoform for a compound
In the development of novel pharmaceuticals, the knowledge of how many, and which, Cytochrome P450 isoforms are involved in the phase I metabolism of a compound is important. Potential problems can arise if a ...
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Article
Open AccessCytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers
The prediction of sites and products of metabolism in xenobiotic compounds is key to the development of new chemical entities, where screening potential metabolites for toxicity or unwanted side-effects is of ...
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Article
Open AccessProbabilistic classifier: generated using randomised sub-sampling of the feature space
