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software for making a model of a protein

software for making a model of a protein - Protocols and Methods Forum

software for making a model of a protein - Post Any Protocol, Method, Technique, Procedure or Tips / Troubleshooting for any Molecular Biology Technique.


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  #1  
Old 05-04-2007, 09:04 AM
Mr Urpradiap
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Default software for making a model of a protein



Dear NG.
I am looking for a graphic tool/software to make a model of how I think 4
domains of a protein resides together in the overall fold of the protein. I
am not looking for an advanced tool to make docking of proteins or any other
calculations on how the domains could fit together. I am simply looking for
a 3D graphic tool where i can build my hypothetical model (publication
grade). If I was good at paintshop I would have made the model from the
ground here (but I am not). I have the four domains as PDB files, that might
make things a bit easier?
Thank you.
Ugi


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  #2  
Old 05-06-2007, 08:13 PM
Dr Engelbert Buxbaum
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Default software for making a model of a protein

Am 04.05.2007, 05:04 Uhr, schrieb Mr Urpradiap <[Only registered users see links. ]>:


Yes it does. There are several tools out there for viewing 3D-protein
models from PDB-files. Appart from those mentioned by others there is also
the Protein Explorer
([Only registered users see links. ]), which
has some nice tutorials on protein structure coming with it.

However, for your purposes DeepView
([Only registered users see links. ]) will probably be the easiest
solution since it can automatically align similar proteins (homolouges or
with/without ligand etc). Output is either as a single TGA graphics, as a
pair of TGAs for right/left eye or as a PovRay-script. And what the
Persistence of Vision Raytracer ([Only registered users see links. ]) makes from such
structures you need to see for yourself to believe it.
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