I hope to get some suggestion, what kinds of protein structure simulation can allow me to analysis the effect to these nonsynonymous in the exon of FGF6 genes?
FGF6 . nonsynonymous SNV FGF6:NM_020996:exon3:c.G563A:p.R188Q
FGF6 . nonsynonymous SNV FGF6:NM_020996:exon3:c.A521T:p.D174V
FGF6 . stopgain FGF6:NM_020996:exon3:c.G514T:p.E172X
FGF6 . nonsynonymous SNV FGF6:NM_020996:exon3:c.C485T:p.T162I
FGF6 . nonsynonymous SNV FGF6:NM_020996:exon2:c.C449T:p.T150M
FGF6 . nonsynonymous SNV FGF6:NM_020996:exon2:c.G445A:p.A149T
FGF6 . synonymous SNV FGF6:NM_020996:exon2:c.C444T:p.Y148Y
FGF6 . synonymous SNV FGF6:NM_020996:exon2:c.C444T:p.Y148Y
FGF6 . synonymous SNV FGF6:NM_020996:exon2:c.T417C:p.V139V
FGF6 . nonsynonymous SNV FGF6:NM_020996:exon2:c.C388G:p.L130V
FGF6 . nonsynonymous SNV FGF6:NM_020996:exon2:c.A358G:p.I120V
FGF6 . . . FGF6 . nonsynonymous
SNV FGF6:NM_020996:exon1:c.G187A:p.A63T FGF6 . nonsynonymous
SNV FGF6:NM_020996:exon1:c.T107C:p.V36A FGF6 . nonsynonymous
SNV FGF6:NM_020996:exon1:c.G86T:p.G29V
Thanks.
•
written
by
Shicheng Guo
Please take a look at my answer here, in particular the section entitled 'Protein modelling (from amino acid sequence)': A: pathogenicity predictors of cancer mutations
Through the link, you can have access to numerous tools that attempt to predict the change in conformation of the protein due to the mutation. You usually have to provide the entire amino acid sequence though.
Kevin
Awesome!! Thanks Kevin.
https://www.proteinmodelportal.org/?pid=modelling_interactive
This is working!!
Great - note that all are for academic / research use only.
Get the simulated protein structure, however, totally don't know what's the difference. What the hell it is...
What did you receive in your email - a PDB file? You can view the site of the mutation in Jmol. I believe that there are functions in Jmol that allow you to search for amino acid residues. Then, you can see if, for example, if differences appear over the wild-type.
Sorry, I am not aware of any automated method to do this.
Thanks Kevin, I checked the simulated structure with Cn3D. Jmol is better than Cn3D?
RasMol vs JMOL vs Cn3D
For more advanced uses, such as command line control, you can install RasMol. Some scientific websites are using JMOL, a Java-based viewer, for rendering molecules in 3-D. JMOL and similar tools may replace Chime eventually, but for now, Chime is the program used most for viewing small molecules from websites.
If you would like to view macromolecules in 3-D, download and install Cn3D. This program should be all you need to visualize proteins of interest. For advanced users, investigate Protein Explorer, a RasMol derivative.
Thank you for the information, Shicheng
Log in to answer this question.