Dear applied scientist,
Swissdock is the online server for molecular docking, the searching and scoring function of this tool is good enough for beginner. after successful docking they provide a ligand-receptor complex file, if this file is uploaded in molecular visualization software, it only show binding cleft and ligand is located on it, without any bonding connection. so, suggest any software which provide the facility of visualization bonds in between ligands and receptors which ae predicted by SWISSDOCK server.
Thanks.
In PyMOL, one can draw lines (solid, dashed, dotted) between atoms or groups; and between 'invisible points in space'; one can use different colors to distinguish different types of interactions. The visualization possibilities are 'inexhaustible.' So, if SWISSDOCK reports these types of interactions in a readable way, one can process them with a PyMOL/Python script.
---
Not a SWISSDOCK user.
Dear Dr. Jadhav,
To visualizr the bonds in between ligands and receptors (which ae predicted by SWISSDOCK server), DS Visualizer is very useful. It provides both 3D and 2D ligand interactions with the receptor.
You may also use Protein-Ligand Interaction Profiler (PLIP), https://projects.biotec.tu-dresden.de/plip-web/plip/.
Thanks.
Hi
You can use Discovery Studio visualizer software (version 16. 1. 0) . this software is free to download.
I prefer biovia Discovery Studio Visualizer for protein - ligand interaction studies.
Among the different software/sites suggested in this discussion, which is most reliable and more accurate?
Sometimes, there are differences in the number and kind of interactions shown by different software/servers for a particular complex.
Could anyone please comment on this?
- Badges
- Science topic
- Similar topics
- Engineering
- Chemical Engineering
- Membranes