But maybe you can have a try: HADDOCK seems to give good results, once you have defined the symmetry of your complex...

See:
Mol. Cell. Proteomics 2010
'Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multi-body docking server' Karaca E. et al.

Cheers,
Annalisa

-----------------------------------------
Annalisa Bordogna
PhD. Student
Università degli Studi di Milano - Bicocca
Milano (Italy)

2010/5/19 Maia Cherney <chern@ualberta.ca>

Docking is very non-reliable.

E. Krissinel (2009). /Crystal contacts as nature's docking solutions/.
J. Comp. Chem., in press; published on-line 6 May 2009; DOI
10.1002/jcc.21303

Maia

humayun scherrif wrote:
> Hello,
>
> Thank you for detailed explanation, surely it is helping me to sort
> out the possibilities. As per your query
>
> a) There are many references that the protein is a Hexamer, but I am
> considering, because the domain which I have got structure, interacts
> with other proteins to make a biological complex, their interaction
> could be important for biological hexamerization of the whole complex
> ( those interacting proteins also exist as hexamer in complex with my
> protein )
>
> b) I coudnt find any hexameric homologue (although there are some good
> homologue structures but they mostly exist as dimer or monomer)
>
> c) the structure is not yet been solved and not reported as yet.
>
> So according your reply, does that mean the only possibility left is
> docking ? because others are not working for me at all.
>
> Thank you again for suggestions.
>
>
>
>
>
>
> On Wed, May 19, 2010 at 6:31 PM, Tsjerk Wassenaar <tsjerkw@gmail.com
> <mailto:tsjerkw@gmail.com>> wrote:
>
>     Hi Humayun,
>
>     Crystallograpic symmetries are often not of much help to construct
>     biologically relevant complexes. Do you have (a) a reference of the
>     hexameric structure, or (b) of a hexameric homologue, or (c) is it
>     only known to form hexamers and is the structure still unsolved? In
>     case of (a), the structure is likely to have a recipe to build the
>     biological unit (possibly as REMARK 350 in the PDB file). In case of
>     (b), you can try to fit copies of the structure onto each chain of the
>     homologue, being aware that that will give you a crude approximation
>     as starting point for further work. And in case of (c), you might want
>     to consider doing some docking.
>
>     Hope it helps,
>
>     Tsjerk
>
>
>     On Wed, May 19, 2010 at 10:26 AM, humayun scherrif
>     <hum.one@gmail.com <mailto:hum.one@gmail.com>> wrote:
>     >
>     > Thank you all for the replies.
>     >
>     > The protein itself makes hexamer which is well documented and proved
>     > structural evidence from other cytoplasmic domains ( my
>     structure is also a
>     > domain).
>     > I have run PISA, but the online PISA server didnt give me output
>     like
>     > standalone PISA in CCP4 (result is mentioned below). Online PISA
>     results
>     > show that "there are not significant dimer interfaces and thus
>     the trimer
>     > structure is because of only crystal packing result"
>     > For homology modeling I didnt get any proper homologs which have
>     hexameric
>     > assembly (I@ Bryn: I cant send you PDB id since its not
>     submitted yet)
>     >
>     >  Analysis of protein interfaces suggests that the
>     following  quaternary
>     > structures are stable in solution (I wonder the DGdiss is
>     positive value, is
>     > it significant to make Hexamer assembly because I couldnt find
>     any help to
>     > find out about the allowed values)
>     >  ----.-----.---------------------------------------.---------------
>     >  Set |  No | Size  Id      ASA       BSA    DGdiss | Formula
>     >  ----+-----+---------------------------------------+---------------
>     >    1 |   1 |   6    0   19917.7    5536.3      3.8 |
>     A(2)B(2)C(2)
>     >  ----+-----+---------------------------------------+---------------
>     >    2 |   2 |   3    1   10722.9    2004.1      6.2 |      ABC
>     >  ----+-----+---------------------------------------+---------------
>     >    3 |   3 |   4    2   14004.2    3014.9      0.5 |      A(2)B(2)
>     >      |   4 |   1    3    4217.5       0.0         -0.0 |      A
>     >  ----+-----+---------------------------------------+---------------
>     >    4 |   5 |   2    4    7506.2    1003.3      7.0 |        AB
>     >      |   6 |   1    3    4217.5       0.0        -0.0 |        A
>     >  ----+-----+---------------------------------------+---------------
>     >    5 |   7 |   2    5    7443.8    1000.8      6.8 |      AB
>     >      |   8 |   1    6    4282.4       0.0     -0.0 |         A
>     >  ----+-----+---------------------------------------+---------------
>     >    6 |   9 |   2    7    7556.5    1008.3      2.0 |      A(2)
>     >      |  10 |   1    8    4227.1       0.0     -0.0 |        A
>     >      |  11 |   1    3    4217.5       0.0     -0.0 |        A
>     >  ----'-----'---------------------------------------'---------------
>     >
>     > Waiting for your reply
>     > Thanks
>     >
>     > H
>     >
>     >
>     >
>     > On Wed, May 19, 2010 at 4:41 PM, Robert Brynmor Fenwick
>     > <robert.fenwick@irbbarcelona.org
>     <mailto:robert.fenwick@irbbarcelona.org>> wrote:
>     >>
>     >> Also, if you would like to try homology modelling then that
>     could work.
>     >> However you would need a couple of hexamer strucutres to start
>     with. It
>     >> would probably take some tinkering with current tools. I would
>     probably use
>     >> an MD approach to solve this problem.
>     >> Sorry I don't have a quick fix this is not my current area of
>     expertise.
>     >> Bryn
>     >>
>     >> Sent from my iPod
>     >> On 19/05/2010, at 09:22, humayun scherrif <hum.one@gmail.com
>     <mailto:hum.one@gmail.com>> wrote:
>     >>
>     >>
>     >> Thank you Bryn for your reply, But I have already tried all
>     possible
>     >> symmetries that it generates, but it does not provide a proper
>     hexameric
>     >> assembly. Does it mean this is due to problems in crystal packing ?
>     >> Is there any alternative way to generate or by homology, which
>     server
>     >> could be suitable ?
>     >>
>     >> Regards
>     >> H
>     >>
>     >> On Wed, May 19, 2010 at 4:02 PM, Robert Brynmor Fenwick
>     >> <robert.fenwick@irbbarcelona.org
>     <mailto:robert.fenwick@irbbarcelona.org>> wrote:
>     >>>
>     >>> There is a symmetry command that will build the crystal
>     symmetry from
>     >>> the pdb header you could then delete the irrelevent molecules
>     to leave
>     >>> the six that you want.
>     >>>
>     >>> Bryn
>     >>>
>     >>> If you have trouble with this I can hunt down the commands in
>     my labbook
>     >>>
>     >>>
>     >>> > _______________________________________________
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>     <mailto:PyMOL-users@lists.sourceforge.net>)
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>     >>
>     >>
>     >>
>     >
>     >
>     >
>     >
>     >
>     ------------------------------------------------------------------------------
>     >
>     >
>     > _______________________________________________
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>     <mailto:PyMOL-users@lists.sourceforge.net>)
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>     >
>
>
>
>     --
>     Tsjerk A. Wassenaar, Ph.D.
>
>     post-doctoral researcher
>     Molecular Dynamics Group
>     Groningen Institute for Biomolecular Research and Biotechnology
>     University of Groningen
>     The Netherlands
>
>
>
>
> --
> Best Regards,
>
> Humayun Sharif
> MS candidate
> Protein Structure and Function Laboratory
> Gwangju Institute Of Science & Technology,
> Gwangju, 500-712, Republic of Korea
> Email: hum.one@gmail.com <mailto:hum.one@gmail.com>
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