[Chimera-users] modeling selected protein mutations to a sequence

Teresa Brito-Robinson Teresa.Brito-Robinson.2 at nd.edu
Thu Apr 2 16:09:46 PDT 2020

Wow great thank you so much!
I will check those sources and tips to continue learning.
Have a great evening!


On Thu, Apr 2, 2020, 6:57 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Teresa,
> Welcome to Chimera!  Although it does not predict 3D structure from amino
> acid sequence only, see part (B) below.
> (A) If you already have a 3D structure such as a PDB file, in Chimera you
> can "mutate" an amino acid side chain from one type of residue to another.
> However, it is only replacing the side chain and does not predict any other
> changes that might occur in the backbone or the rest of the structure.  It
> is a first-order simplistic approach that can suggest whether the new side
> chain fits into or clashes with the rest of the structure, or whether it
> might form H-bonds.
> This virtual mutation of individual amino acid sidechains can be done with
> either the "swapaa" command or the Rotamers tool (in menu under Tools...
> Structure Editing):
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html
> >
> There's an example of using Rotamers in the "Structure analysis and
> comparison" tutorial:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
> (B) if you have an entire protein sequence for which you want to predict a
> structure, in Chimera you may be able to use the Modeller web service.
> However, to use it would need to have two things: (1) a related 3D
> structure to use as "template" for comparative modeling, and (2) a sequence
> alignment that includes both your sequence (the "target") and the sequence
> of the template structure.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>
> Some possible ways to get these necessary inputs are described here, with
> links to related tools:
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#approaches
> >
> For example, you could enter your sequence in the Blast PDB tool to find
> related structures and also give you an alignment of the two sequences.
> However, there are lots of other programs and web services (not connected
> to Chimera) for protein structure prediction, so you may want to search the
> web and/or literature to get a better idea of what is available.  It is
> also common to use some other program to predict the structure, and then
> open the resulting PDB file in Chimera for further analysis.  If there
> aren't any 3D structures related to your sequence, then you would have to
> use a de novo modeling program, as opposed to the comparative (homology)
> modeling described in (B).
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Apr 2, 2020, at 1:37 PM, Teresa Brito-Robinson <
> Teresa.Brito-Robinson.2 at nd.edu> wrote:
> >
> > Hi Chimera users,
> > I am trying chimera for the first time and my question is:
> >
> >       • How can I change (substitute) specific amino acids within an
> uploaded protein sequence to mimic a missense mutation?
> >
> >       • Or how can I enter a whole new custom made protein sequence into
> chimera, so I can probe different variants of a protein sequence.
> > I don't know how to make the file like pdb (protein database) so I can
> fetch my custom sequence?
> >
> > Thanks!
> > Teresa
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