On 26/08/2011 1:16 AM, Steven Neumann wrote:
Dear Gromacs Users,
I want to do some simulations of the protein (its N anc C terminals)
which crystal structure does not exist.
There will normally be reasons why the termini do not have a defined
structure - often that this are in fact disordered. That will make your
life doing simulations considerably more difficult, and not just in
choosing a starting structure.
I submitted the sequence to www.proteinmodelportal.org
<http://www.proteinmodelportal.org/> obtaining different structures
based on different proteins from Protein Data Bank. For instance my N
terminal has 180 aa. Obtained models covers %Seq id of 78% for 36
residues, 68% for 36 different residues, 62% of 36 another residues
and many other models below 50%. The website provides you with the PDB
files of your query so sounds perfect as you do not have to mutate
every residue one by one.
The question is whether this is efficent and provide a good result to
use such protein in my simualtions? Is this app. too big?
Depends what simulations you plan - but very likely you will not be able
to study more than one or two candidate structures.
What are the other ways to overcome this problem (obtain structure of
the protein which crystal structure does not exist?
Protein structure prediction is a field all of its own for a reason.
It's hard.
Mark
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
