VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Mar 31 2016 - 14:06:46 CDT

Just one note: all of the posters are correct that if you actually want to predict a real protein structure, you’re looking at a real research problem — several excellent suggestions have been made.
But if you just want to build a toy peptide, short alpha helix, etc. you can use the molefacture plugin, which lets you paste in a sequence and build a corresponding structure with preset ramachandran angles, which can then be written as a pdb.

Best,
Peter

> On Mar 31, 2016, at 11:10 AM, Stefan Doerr <stefdoerr_at_gmail.com> wrote:
>
> 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
>