How to visualize active site residues and interactions?

Hi,

Is it possible to visualize active site residues and interactions with bound or docked ligands? Haven't been able to find this.

Thanks/Evert

[jacobdurrant]

Hi Evert.

Unfortunately, there is not currently a way to visualize only active site residues and interactions. This is a feature I would like to add in the future. You can visualize all receptor atoms, and then focus on the ligand. That will zoom in on the ligand and allow you to visually inspect the position of the receptor atoms relative to the ligand, but it doesn't quite do auto-detection of interactions.

I'm actually currently working on a beta version of the next iteration of MolModa. You can find it here: https://durrantlab.pitt.edu/apps/molmoda/beta/

It can identify interactions between proteins and ligands using a remote call to the PoseView server. See the Binding menu, Interaction Diagram submenu, if you want to check it out.

Hope this helps. Take care.

Thanks for your quick reply. The PoseView approach works in principle but is slow of course, and difficult to compare multiple ligands within Molmoda.

BW/Evert

[martinj80]

Hi Evert.

Unfortunately, there is not currently a way to visualize only active site residues and interactions. This is a feature I would like to add in the future. You can visualize all receptor atoms, and then focus on the ligand. That will zoom in on the ligand and allow you to visually inspect the position of the receptor atoms relative to the ligand, but it doesn't quite do auto-detection of interactions.

I'm actually currently working on a beta version of the next iteration of MolModa. You can find it here: https://durrantlab.pitt.edu/apps/molmoda/beta/

It can identify interactions between proteins and ligands using a remote call to the PoseView server. See the Binding menu, Interaction Diagram submenu, if you want to check it out.

Hope this helps. Take care.

Hi,

I am liking this software a lot. It is easy to use.

For the interactions, I am not sure how hard would it be but if you switched from 3Dmol.js to mol*, you could identify interactions pretty easily and get a state-of-the-art graphics as well.

Also prolif can calculate interaction fingerprints and already has 3Dmol.js integration for the interactions implemented. This could also be helpful for post docking processing.