Binding Constant Determination


I am just starting to learn how to use the MDWeb simulations on the website. I was wondering if anyone may provide insights upon how to set up a run. I am looking to simulate the binding interactions between a peptide and a protein and to extract out the binding distances and binding parameters. Thanks for helping !


Hi Alex,

please take a look at the MDWeb help section to start with the MD setup process, in particular to the MD setup tutorial.

I would also recommend to take a look at the BioExcel Building Blocks (biobb) website, which is a more recent library that can help you on the MD setup and run processes.

Thanks for your interest in our tools!