3D structure predict

[lubo lu]

Hi Everyone,
I am now need to predicting the 3D-structure of a short
terminal(about 20 aa) in a big protein(about 800 amino acid).I wonder
how can I do it?
Use which software or server? Use what kind of method?
or any suggestion and short tips are welcomed.Thanks

LB

[John Hoey]

Hi LB:
You can definitely do this with DeepView Swiss-modeler PDB.
John

[lubo lu]

the protein has some domains which has solved stucture in pdb
separately,but the loop between domains, especially that is what I
interested in ,has not solved and no template pdb to comparative
modelling .How to predict the loop stucture or estimate whether it
really has stable stucture?and deepview or swissmodel can do this ?

2008/10/19 John Hoey <jh...@mdlab.com>:

[Steven Platt]

I'd recommend looking for a good loop prediction tool/server and then
stitching this into the structures you already have.

I can only find ArchPRED (http://manaslu.aecom.yu.edu/loopred/) which
requires a structure to work on ... there must be others out there
somewhere ... aren't there?

Steve
HPA Bioinformatics
UK

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[Galina Brychkova]

Hi,
I wish to modify some conserve amino acids in my protein sequence.
Can you please direct me to the program or table, which can help me to
decide to which amino acids I shell substitute the selected one and not
to change the confirmation, and charge of the protein?
Thank you very much in advance,
Gala

[Linlin Yan]

Maybe you can use SwissPDBViewer to show your origin protein
structure, and then try to change amino acid(s) and simulate the new
structure by computer. About amino acids' property, such as charge, I
think you could refer some textbook about biochemistry.