I need to run generalized simulations rather than ones for specific molecules.
Thanks Danish, for attempting to answer my question.
Something like that, yes, but not exactly.
I want to model how enzymes may attack functional groups. The input molecules will be generalised chemicals like R-COOH, R-COONa, R1-O-R2, hydrocarbons and more complex molecules. I want to simulate how enzymes may act at and degrade these into various products. For this purpose, I wanted to know if there is a standardised representation to depict structures available. As far as I can see, InChI representation is very molecule specific, but I am more interested in exploring the kinetics for an entire class.
If you want to study the structural aspects of the generalized chemicals you mentioned above and to find the effect of enzyme on these chemicals then you should try pdb file format as you can generate the 3D conformation of the chemical entities together (entire class) and then study them in different visualizers. Further you can study their effects on the enzyme or other way round by MD simulation but to confirm the hypothesis you will have to perform a wetlab analysis. Hope this helps you.
Regards
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