IUBio

Free software to display protein secondary structure in 3D view?

Dr Engelbert Buxbaum engelbert_buxbaum at hotmail.com
Tue Mar 9 08:14:22 EST 2004


bigc wrote:

> Hi Gurus,
> 
> I'm a newbee to bioinfomatics. It seems that via the secondary
> structure we can roughly predict the protein's 3D structure. 

We can't. We can not even predict secondary structures very well.

> Then is
> there free software (better open source) can display a file like this:
>         70        80        90       100       110       120
> .....:....x....:....x....:....x....:....x....:....x....:....x
> VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG    
> 1236136_1236137
> EEECCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCEECEEEEECCCCCCCCCCCCCCCCCC     BPS
> EEEHHHHHHCCCCEEEHHHHHHHHEHEECCECCCEECCECCEEEECCCCCCCCCHHHCHC     D_R
> EEEECCCCCCCHHHHHHHHHHHHHEEEECCCCCEEEECEEEEEEECCCCCCCCEEECCCC     DSC
> HHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCEEEEECCCCCCCCCEEEECC     GGR
> HHHHHHHCCCHHHHHHHHHHHHHHHEEEECCCEEEEEEEEEEEEECCCCCCCCEEEECHC     GOR
> ECCCCCCCCCCCCCCCHHHHHHHHEEEECCCCCEEEECCCCEEEECCCCCCCCCCCCCCC     H_K
> EEEEECCCCCCCEEEEEEEEECEEEEEEEEEEEEEEEEEEEEEEEECCCCCCCEEECCCC     K_S
> EEECCCCCCCCCCCCHHHHHHHHHEEEECCCCCEEEECEEEEEEECCCCCCCCCEECCCC     JOI

If you want to look at protein 3D structures, get a program like protein
explorer, Swiss-PDB or rasmol. Then download the 3D-coordinates of your
protein from the PDB database (protein explorer contains an easy
interface for searching).

If you just started, protein explorer is good enough for you, the other
programs you only need to make publication quality pictures.





More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net