protein docking

[lordy99]

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

[molecule2005]

Hi Lordy!

Here are a few that I found:

ZDOCK

Structure based drug design and molecular modeling

Other sites of interest:
http://mgl.scripps.edu/people/gmm/
http://www.lce.hut.fi/teaching/S-114...2/Protdock.pdf

[lordy99]

Originally Posted by molecule2005

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

[moleculardude]

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.

[lordy99]

i could get correct results with GRAMM (link from the jena page) but i am still on the search for more dockingsoftware to compare

[moleculardude]

Any news on what you are going to use Lordy?

[lordy99]

Originally Posted by moleculardude

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 ...

[Ezgi]

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 !!!!

[biochemi]

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