I have a dimeric protein 3HHZ.....to generate the dimer foll transformations have to be made....the problem is that this is an identity matrix,so will not change anything...can anyone help with this??

how can i get the asymmetric unit to generate dimer??


REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B † † † † † † † † † † † † † † † † †
REMARK 350 † BIOMT1 † 1 †1.000000 †0.000000 †0.000000 † † † †0.00000 † † † † † †
REMARK 350 † BIOMT2 † 1 †0.000000 †1.000000 †0.000000 † † † †0.00000 † † † † † †
REMARK 350 † BIOMT3 † 1 †0.000000 †0.000000 †1.000000 † † † †0.00000 ††

On Fri, Feb 25, 2011 at 6:40 PM, Hongbo Zhu <hongbo.zhu@biotec.tu-dresden.de> wrote:
Hi, Kanika,

are you looking for biological units of proteins when you say stable dimer? If this is the case, I recommend the page:

http://pdbwiki.org/index.php/Biological_unit
at the bottom of the page you can find four very useful servers for the determination of biological units of proteins (PQS is not updated anymore):
† †The Protein Quaternary Structure Server (PQS) [2] or [3]
† †The Macro-Molecular Structure Database (MSD) [4] or [5]
† †The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6]
† †Protein quaternary structure investigation (PiQSi) [7]

As a matter of fact, the PDB also provides the biological assembly of each PDB entry for download. More information can be found at:
http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html

If your protein is not from the PDB, you can still try pisa ( http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts protein coordinate files uploaded by the users and determines the "stable dimer" or else-mer of your protein.

hope these help!
hongbo


On 02/25/2011 01:46 PM, kanika sharma wrote:
Hi,
i am working to generate a dimer of my protein..I have made a duplicate
of my protein....Can any one tell me how to rotate my molecule to get
maximum stability..???


Regards..
Kanika



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--
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics

Technische Universitšt Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany

Tel.: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail: hongbo.zhu@biotec.tu-dresden
Webpage: www.biotec.tu-dresden.de