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Depends whether you work with named selections which is preferable and helpful if you want to use this Pymol session for future images. In this case, use the distance command for your two selections, one being the N of the K in your ligand and the other the O of the E of your protein. Full syntax and examples here: https://pymolwiki.org/index.php/Distance If ...


3

Asking how to visualise the disordered region of a protein is a bit like asking how to visualise the location of an electron. An intrinsically disordered protein, by definition, has regions that are disordered. In other words, their location is variable under observation, so they cannot be precisely placed in a 3D model.


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I believe PDB2PQR CLI will do the work wonderfully. Don't let the name trick you: PQR files are organized like PDB ones. Under the hood it runs propka, which is state-of-the-art for predicting a protein residues protonation state. The best part is that you can use PDB2PQR web server and they will give you the corresponding CLI arguments for each option you ...


2

It is best to contextualise the numbers. -1 kcal/mol is about the potential energy gained from a hydrogen bond —technically described in the r^6 part of the Lenard–Jones term, it is also the average collision energy of a water molecule at 37°C as that is RT ($\frac{k_b\cdot T}{N_A}$, wiki)under a Maxwell–Boltzmann distribution. A salt bridge –2 kcal/mol (...


1

Your title says holistic. This is a tad problematic as there's layers upon layers. Say, post-translation regulation, inhibiting metabolites, interacting protein etc. That is why when talking of an enzyme inhibitor, at the biochemical level one speaks in terms of k_i (inhibition constant), while at the cellular level ("holistic") one talks of IC50. ...


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