Enzymatic Mechanism Explorer

Welcome to a demo of a graph tranformation based enzymatic mechanism explorer (see this article for details). The demo currently allows you to construct a state space for a given reaction and than sample mechanisms from the state space. The state space construction relies on a graph transformation tool for chemistry called MØD and rules derived from the M-CSA database.

State Space Construction

To construct a state space, you may use the build_state_space function (see example). The function allows you to specify a reaction as a Rhea database entry, the catalysts to be used for the mechanism (graph A) and the maximum length of the mechanism.

The example shows how you can load predefined amino acid tautomers. Any other catalyst in the format of a MØD graph is acceptable, however, we can not guarantee it will be properly recognised by our rules, unless the same tautomer appears in the M-CSA database. The demo enforces a strict timeout. We therefore suggest using relatively small mechanism lengths (up to 6). Additionaly, the state space is contructed by combining forwards and backwards expansion, the length of the mechanism should therefore be even. Odd lengths might lead to unexpected regsults.

We currently do not visualise the state spaces, the printed summary file will therefore be empty. Instead, information about the state space can be printed using the print_info method. (Note that we only prune the state space itself for the relevant state spaces, not the underlying reaction network.)

Mechanism Sampling

Mechanisms can be sampled using the sample_mechanisms function (see example). The function requires a state space to sample and allows you to choose the number of mechanisms to print. The sampling is done by searching for the shortest mechanisms first.

The printed mechanisms appear in the summary file. The mechanisms are printed as traces in the reaction network.

Demo

To run the code in the editor, press the Run button. You can abort your run with the Kill button. After a successful run, a summary link will appear where you can access a PDF with the figures you have printed. During the run the terminal on the right will show the exact output of running your script, meaning any print calls will show up there.

Source Code

The source code behind this demo is available here.

The modified version of MØD is also made public in this branch.

Note If the frame below is empty the demo server is temporarily offline.