search

pharmai / plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
http://plip.biotec.tu-dresden.de
GNU General Public License v2.0
445 stars 102 forks source link

interesting related project #35

Closed UnixJunkie closed 6 years ago

UnixJunkie commented 6 years ago

Hello,

At RCSB, they have a ligand viewer nowadays: https://www.rcsb.org/3d-view/1OXR then choose Ligand View and select AIN (aspirin).

They can detect all those interactions: Hydrogen Bonds (blue) Halogen Bonds (turquoise) Hydrophobic Contacts (grey) Pi Interactions (orange, green) Metal Interactions (purple)

Does plip have all of them?

The molecular viewer is open source: https://github.com/arose/ngl

Plip is even more useful because it is a standalone program one can run from the command line.

Thanks, F.

UnixJunkie commented 6 years ago

some doc on the definitions they use is here: https://www.rcsb.org/pages/help/3dview#ligand-view

ssalentin commented 6 years ago

Thanks for the comment. Yes, I'm aware of the new PDB viewer and think they did a great job for visualizing complexes.

PLIP supports all of the listed interactions and additionally electrostatic interactions (salt bridges) as well as water-mediated hydrogen bonds (water bridges).

You can see the definitions used for PLIP here

As you already stated, PLIP can be also run from the command line and provides - next to visualization - also parseable XML files, which lets you integrate our tool in bioinformatics workflows.

UnixJunkie commented 6 years ago

thanks for the details

UnixJunkie commented 6 years ago

I've dreamed about a tool such as plip. This is extremely nice for the chemoinformatics and structural bioinformatics research people. And having it in open source is super cool. Thanks a lot!

ssalentin commented 6 years ago

Thank you!