3D view of protein structure from aa sequence-I need a program to see it

[meli]

Hi all!

 

I have a new protein sequence and I would like to know if someone have tried or know some program that could predict theoritically the 3D structure from the aminoacid sequence. I found some stuff at google.. but those are freaking complicated...

 

Thanks

[MoMo]

Hi all!

 

I have a new protein sequence and I would like to know if someone have tried or know some program that could predict theoritically the 3D structure from the aminoacid sequence. I found some stuff at google.. but those are freaking complicated...

 

Thanks

I'm no expert at protein conformations, but predicting the tertiary or quaternary (sp?) stucture of an a.a. sequence, depending on the length of your sequence can be quite a complicated process possibly requiring super computers to estimate the final structure. Since there are so many factors that affect the final structure, many variables have to be considered to compute the final structure.

 

but if your a.a. sequence is simple then you might be able to use regular pc software, but it is still complicated.

[Bluenoise]

Yeah there isn't anything out there that can do this even to the slightest degree of acuracy.

[clipper565]

maybe you could put your sequence into swiss model and see what happens(http://swissmodelexpassy.org), it'll take a few days for them to get a result to you, but you can download 'deep view' and see a three dimensional model which you can manipulate.

 

Another site you could use is PredictProtein.(http://www.predictprotein.org)

 

G'luck, all you have to do with either one is copy and paste, preferably with the sequences already converted into protein sequences (use something like 'generation' to convert it (http://compbio.ornl.gov/generation), again, it's pretty easy.

 

There are even programs that can determine specific elements of interest, depending on what you want to look for; yet the one through predictprotein uses quite a few different interfaces all at once...g'luck.

[andie]

there is this program called Rasmol... not sure if it will help... here is a link to my professor's website with a link to download it.. its under Rasmol program

http://www.chemistry.lakeheadu.ca/mackinnon/1110/Chap22.html