I want to see the change in binding ability of the enzyme with the substrate in presence of a probable drug molecule insilico. Where can I find reliable information to learn about the basics from the start?
That depends on what you are interested in.
- If you just want to understand how the concentrations of enzyme, substrate and inhibitor affect reaction velocities (that is, enzyme kinetics), you can do that with Monte-Carlo simulations. This is covered in text books on model building in biology. The statistical system R (https://cran.r-project.org/) has the ability to perform such studies.
- If, however, you are interested in how binding of substrates and inhibitors changes the molecular structure of the enzyme, then you have to perform molecular modelling. This is theoretically complicated and numerically expensive. A.R. Leach: Molecular Modelling, 2nd ed., Harlow et al. (Pearson) 2001 would be a text book that covers this. Be warned though: In my personal experience, even for very simple problems, the results of such simulations have only limited resemblance with reality. For example, the 3D-structure of bilirubin is known from X-ray crystallography (doi:10.1098/rspb.1978.0066). The simulation with Avogadro (http://avogadro.cc/) will not reproduce it.
In Silico analysis is all about computational biology. Like Engelbert said, it depends on what you want to do. For gene expression analysis, see the link.Article In silico gene expression analysis - An overview
For In Silico analysis of proteins, see the attached file. For the challenges you might encounter see the attached document. The databases could be found in the document attached.
Thank you!
So the situation is that I have the AA sequence of the enzyme, but a confirmed 3D structure is unavailable. So this means I would have to use a simulated version of the molecule? How do I obtain this?
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