I want to find the binding modes/site of chemical inhibitors with the protein of interest..?
Http://www.modelling.leeds.ac.uk/pocketfinder/ follow the link to just now pocket/binding site of your protein
try out the DockVision - docking package created by scientists for scientists by including Monte Carlo, Genetic Algorithm, and database
screening docking algorithms.
link
http://dockvision.com/
also have a look through this link
http://www.imb-jena.de/~rake/Bioinformatics_WEB/dd_tools.html
thank u
@Venkateswara Swamy @Muhammad Sulaman Nawaz@ Rajashri Bhairamadgi, Thank you all very much for your kind and prompt reply to my query. Thats so nice of you. I would surely try out the suggested docking tools by you. Further, since i am new to this field, i may need your valuable guidance in using docking tools, i would concern you again. So i hope you will extend your help to me.
Thanks.. Thanks a lot you all..!!
you can try autodock http://autodock.scripps.edu/
If you using window platform you must install Cygwin http://www.cygwin.com/
to help autodock run on winsdows platform
you can try Schrodinger,autodock,discovery studio.. upto my knowledge i used Schrodinger i got best results when compared to Autodock.
if its protein protein docking or DNA protein docking ... go for HEX and Auto dock ... best one is GLIDE schrodinger product
You can mail me your queries on [email protected]
where as if u want to identify the cavity regions u can used Q-Site finder server online, where as for docking u can go with Free tools : Arguslab, Dock, Autodock, and many more, if u r looking for Protein- protein docking go with Hex.....
You can try with autodock software it is freely available and it is very good
first u have to use GLIDE ...... if it is protein and small molecule docking ..
Rosetta FlexPepDock
try out this docking server-Rosetta FlexPepDock, consists of two alternating modules that optimize the peptide backbone and rigid body orientation, respectively, using the Monte-Carlo with Minimization approach.
http://flexpepdock.furmanlab.cs.huji.ac.il/index.php
Locating Binding Sites in Protein Structures
http://www.chemcomp.com/journal/sitefind.htm
http://sts.bioengr.uic.edu/castp/index.php
thanks
hi u can use Hex software for docking.It is freely avaliable.........
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