Is there any method or software to do ligand-ligand docking and is there any software for searching ligands for any specific protein and proteins for any specific ligand?
http://bip.weizmann.ac.il/toolbox/structure/binding.htm
visit this link it will be very helpful for you about docking softwares.
There are many sites which give complete details about ligands and proteins for any specific targets...for ligands sites like pubchem, chemspider, zinc, drug bank are very useful and for finding protein partners sites like stich, string are helpful, moreover literature review in both cases would be very useful
You should have a look through some of the answers on this previous post, they might help you out!
http://www.researchgate.net/topic/Bioinformatics_and_Computational_Biology/post/Online_servers_to_go_the_protein-ligand_docking
http://bip.weizmann.ac.il/toolbox/structure/binding.htm
visit this link it will be very helpful for you about docking softwares.
There are many sites which give complete details about ligands and proteins for any specific targets...for ligands sites like pubchem, chemspider, zinc, drug bank are very useful and for finding protein partners sites like stich, string are helpful, moreover literature review in both cases would be very useful
Actually I am working on Pseudomonas aeruginosa virulence factor Pyocyanin and I wish to analyse its interactions with cellular proteins. There are many different bioactivities attributed to this compound so there must be many interactions with cellular proteins. I wish to study those interactions via docking if possible :).
It would be possible to analyze interactions between pyocyanin with cellular proteins via docking studies, I would recommend you to use autodock tool for dockings
Molegro Virtual Docker program is good one for Protien-ligand docking.
As an open source Autodock4.2 would work very accurately for you, before specifying ligand & proteins, do analyse them using http://www.ebi.ac.uk/pdbsum/ and Pocket finder....
If 3D structure of your target protein is available than you can perform docking using autodock vina software.
If u want protein ligand docking than use autodock vena, if protein protein than use z-dock, if you want network study than use protein protein interaction toll.
I would recommend Autodock for protein ligand docking, because its an open source. If commercial means you can go for Glide module in Maestro.
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