Protein Structure Prediction - HELP!! (Sep/07/2005 )

Hi all,

i am looking for a software or a web site or SOMETHING to help me predict the 3d struc of the protein. The structure is know in PDB, but i want to see what effect certain mutations will have on the sturcture.

A lot of sites give me lots of numbers etc, but i am looking for something visual.. does anyone know if thats possible??

Any suggestions would be a great help in getting me un-stuck!

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Try use swiss-pdb software. It can predict 3d structure based on sequence similarity (> 80%). So if you are mutating your know structure, you've already have that similarity there, so I think it will work if you just fold and overlap the mutated sequence with the original structure.

Haven't done such yet, but I think it'll work. Try it out.

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I have used swissmodel:

http://swissmodel.expasy.org/

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you might find this list helpful. good luck.

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u can try Cn3D in NCBI website
u can download it onto ur compt and use it when ever u want
plus there is RASMOL and others

u can do mutations and visually see the difference by indicating colours
of course u need the PDB file in ur compt or u will need to konw the PDB id of the protein
good luck!!

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