[gmx-users] Obtaining protein structure

Steven Neumann s.neumann08 at gmail.com
Thu Aug 25 17:16:25 CEST 2011

Dear Gromacs Users,

I want to do some simulations of the protein (its N anc C terminals) which
crystal structure does not exist. I submitted the sequence to
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?
What are the other ways to overcome this problem (obtain structure of the
protein which crystal structure does not exist?

Thank you in advance,

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