<div>Thank you for your help. I want to calculate binging free energy of small molecules to protein termini. </div>
<div class="gmail_quote">On Thu, Aug 25, 2011 at 4:22 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
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<div class="im">On 26/08/2011 1:16 AM, Steven Neumann wrote:
<div>Dear Gromacs Users,</div>
<div>I want to do some simulations of the protein (its N anc C terminals) which crystal structure does not exist.</div></blockquote><br></div>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.
<div>I submitted the sequence to <a href="http://www.proteinmodelportal.org/" target="_blank">www.proteinmodelportal.org</a> 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. </div>
<div>The question is whether this is efficent and provide a good result to use such protein in my simualtions? Is this app. too big? </div></blockquote><br></div>Depends what simulations you plan - but very likely you will not be able to study more than one or two candidate structures.
<div>What are the other ways to overcome this problem (obtain structure of the protein which crystal structure does not exist?</div></blockquote><br></div>Protein structure prediction is a field all of its own for a reason. It's hard.<br>
<font color="#888888"><br>Mark<br></font></div><br>--<br>gmx-users mailing list <a href="mailto:firstname.lastname@example.org">email@example.com</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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