VMD-L Mailing List

From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Thu Mar 31 2016 - 10:16:11 CDT

That being said, the model you will get out of these methods can be from
great to absolutely useless (especially if it's a protein with very distant
homologues) and you will never know any better. So tread with care.

On Thu, Mar 31, 2016 at 5:10 PM, 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
>>
>
>