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 <ch...@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 <tsje...@gmail.com > > <mailto:tsje...@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....@gmail.com <mailto:hum....@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.fenw...@irbbarcelona.org > > <mailto:robert.fenw...@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....@gmail.com > > <mailto:hum....@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.fenw...@irbbarcelona.org > > <mailto:robert.fenw...@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 > > >>> > > >>> > > >>> > _______________________________________________ > > >>> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net > > <mailto:PyMOL-users@lists.sourceforge.net>) > > >>> > Info Page: > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >>> > Archives: http://www.mail-archive.com/pymol- > > >>> > us...@lists.sourceforge.net <mailto: > us...@lists.sourceforge.net> > > >> > > >> > > >> > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > > > > > > > > > _______________________________________________ > > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net > > <mailto:PyMOL-users@lists.sourceforge.net>) > > > Info Page: > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > Archives: > > http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > > > > > > > -- > > 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....@gmail.com <mailto:hum....@gmail.com> > > ------------------------------------------------------------------------ > > > > > ------------------------------------------------------------------------------ > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >
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