Also consider Raman and FT-IR spectroscopy as well as the results form consensus secondary prediction servers and biological information in the literature to assign secondary structure restraints to specific residues. This task requires a lot of biophysical intuition so I cannot help you further in this regard.
Thomas On 9 January 2012 12:37, Steven Neumann <[email protected]> wrote: > Hi, > > Thank you! So what kind of exepriments will you suggest? Is CD enough? I > can also perform Microcalirometry for secondary structure. > The one chain (N terminal) is 180 amino acids and second (C terminal) is > 150. They have similar sequence as they are polyglycine peptides which are > known to form loops (beta loops). > > Steven > > On Mon, Jan 9, 2012 at 9:52 AM, Thomas Evangelidis <[email protected]>wrote: > >> Hi, >> >> The problem with I-TASSER is that you cannot use the desired templates >> for threading. The server has an option to exclude specific templates but >> it will always find distant "homologues" to use to create restraints and >> fragments. ROBETTA has also the same disantvantage. I would recommend using >> standalone programs like Rosetta (for ab inition structure prediction or >> homology modeling), MODELLER (homology modeling), etc. Also collect as many >> experimental data as possible and use them as restraints during modeling. >> Termini are very flexible and structure prediction is very chalenging for >> these parts. >> >> By the way, what is the length of the missing part? >> >> Thomas >> >> >> >> >> On 9 January 2012 11:29, Steven Neumann <[email protected]> wrote: >> >>> Thank you Emanuel. I will try what you have suggested and I think I will >>> try to confirm it exeprimentally to be sure about my initial structure. >>> This is terminal which is highly flexible and beta loops are very common >>> for this sequence. >>> Thanks a lot! >>> >>> Steven >>> >>> On Mon, Jan 9, 2012 at 9:19 AM, Emanuel Peter < >>> [email protected]> wrote: >>> >>>> Hi Steven, >>>> >>>> There is a difference between homology modelling and ab-initio >>>> modelling. >>>> With SWISS-modeller or ITASSER you have a lot of templates, which are >>>> searched >>>> automatically. In case, if this part of the sequence does not have any >>>> homology, >>>> then your model contains loops and has no secondary-structure as >>>> alpha-helices >>>> or beta-sheets. >>>> As one possibility you could model these parts by ab-initio modelling >>>> (ROBETTA). >>>> Another possibility could be the MODELLER. >>>> From the bunch of models you should decide yourself, what's the most >>>> reasonable one. >>>> [ Radius of gyration (SAXS). Secondary structure prediction (SSPRED) ] >>>> >>>> I am not sure if this could help you further and of course I am not an >>>> expert in >>>> this field. I do not want to open a huge discussion with personal >>>> attacks as it >>>> is usually done in this list. >>>> >>>> Bests, >>>> >>>> Emanuel >>>> >>>> >> -- >> >> ====================================================================== >> >> Thomas Evangelidis >> >> PhD student >> >> Biomedical Research Foundation, Academy of Athens >> >> 4 Soranou Ephessiou , 115 27 Athens, Greece >> >> email: [email protected] >> >> [email protected] >> >> >> website: https://sites.google.com/site/thomasevangelidishomepage/ >> >> >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: [email protected] [email protected] website: https://sites.google.com/site/thomasevangelidishomepage/
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