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protein docking

protein docking - Bioinformatics

protein docking - Have questions about bioinformatic tools or databases? Post questions here. Discuss and post interesting bioinformatics information.


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  #1  
Old 12-15-2006, 12:20 PM
Pipette Filler
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Default protein docking



for my phd thesis i am searching for a protein docking software. i have 2 complexes with each around 200 residues. the position of the binding site is known. the software should just perform a little rotation in x,y and z but no translational moves. it should also return some sort of "fitness value" for the docking position. i want to compare the binding affinity of one receptor to many very similar ligands. so i think a geometric scoring function is not sufficient...


any suggestions?

thx
lordy
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  #2  
Old 12-19-2006, 07:58 AM
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Default Re: protein docking

Hi Lordy!

Here are a few that I found:

[Only registered users see links. ]

[Only registered users see links. ]

Other sites of interest:
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[Only registered users see links. ]
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  #3  
Old 12-19-2006, 08:17 AM
Pipette Filler
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Default Re: protein docking

Quote:
Originally Posted by molecule2005 View Post
Hi Lordy!

Here are a few that I found:

...

...

Other sites of interest:
...
thx - sorry for mutilating your post but i am not allowed to post URLs before i have 15 posts

- i already tryed autodock, but the problem seems to be that it doesnt like more then 6 different atom types
- i also tryed zdock which runs without any problems but unfortunately the result of the docking was totally wrong (altough i gave it the binding site)

but this overview webpage from jena looks nice - i guess i will work trough that
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  #4  
Old 12-19-2006, 05:06 PM
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Default Re: protein docking

welcome to the forums!!

Its ok actually we are sorry as we had to stop spammers from posting URLs in the forum. I guess only way is to get people to post 15 times...

I will try asking my protein docking friends what software they use.
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  #5  
Old 12-20-2006, 09:40 AM
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Default Re: protein docking

i could get correct results with GRAMM (link from the jena page) but i am still on the search for more dockingsoftware to compare
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  #6  
Old 12-21-2006, 09:38 AM
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Default Re: protein docking

Any news on what you are going to use Lordy?
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  #7  
Old 01-02-2007, 08:47 AM
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Default Re: protein docking

Quote:
Originally Posted by moleculardude View Post
Any news on what you are going to use Lordy?
the only softwaretools which could obtain the (pre-known) correct results where GRAMM, BiGGer and Escher-NG. where BiGGER is only useable with a GUI and not automatically... then i left for holidays

now i am trying to get the trail ICM docking software (where the full version is unfortunalty very expensive).

so i am still working on it ...
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Old 05-11-2007, 09:57 PM
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Default Re: protein docking

Hi, I am a masters student and need a protein-docking software. I have two proteins with known structures and interaction sites.
The problem is I only know how to use Swiss-PdbViewer as a software. I looked around the internet and found couple of docking software but I couldn't work them. I need help !!!!
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  #9  
Old 06-15-2007, 05:30 AM
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Default Re: protein docking

hi,
autodock is a good software for protein docking, u can use that one
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