VMD-L Mailing List

From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Thu Mar 31 2016 - 10:10:54 CDT

Using VMD no. But sure there are many programs that can build protein
structures purely from the sequence.

https://en.wikipedia.org/wiki/List_of_protein_structure_prediction_software

The whole CASP competition is based around that. Too big a field for me to
get into detail but from when I took part in CASP I remember I-TASSER being
one of the top methods.

On Thu, Mar 31, 2016 at 4:47 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> You need more than just a protein sequence. I don't believe that any
> program exists which uses only the protein sequence to generate structure.
> You should try homology modelling. That requires a query sequence (for
> which the structure is missing) - and a target sequence and structure.
> Homology between the sequences is used to "predict" the missing structure
> using the target structure as a template. Many methods exist for this.
>
> Not sure if VMD can do this (it should be - it has all the relevant
> plugins) but you can use Modeller. You might also want to wait for someone
> else to add a more useful reply to this. However if you want to use just
> the sequence --- you maybe in for a very very long wait.
>
>
> On Fri, Apr 1, 2016 at 2:40 AM, chin chun <chinchun19_at_gmail.com> wrote:
>
>> Dear VMD users,
>>
>> Can we build (pdb) a protein from a protein sequence using VMD. If not
>> could you please suggest any free software.
>>
>> Thanks in advance!
>> Chinchun
>>
>
>
>
> --
> Best,
> /A
>