I want to get the 3D structure for a peptide of 13 amino acids.
What is the best server that can help me?
How can I construct a modification to that peptide to get S-S bond in it? Should I build it first then modify and minimize? or there is servers that built it with the modifications.
Is there is a database for peptides using as inhibitors for proteins that can I search?
Thanks
Abdo
for a very basic 3d visualization you can use chemdraw, chembio3d, but if you want a real conformational search you should use a more costly software like maestro ect....
Hi Abdo,
I recommend UCSF Chimera:
https://www.cgl.ucsf.edu/chimera/
To build 3D model of a peptide, do like this:
Tools -> Structure editing -> Build structure -> Add peptide -> Peptide sequence (like ADEKHWAAAAAAA) -> Apply -> OK
Tools -> Structure editing -> Minimize structure -> Minimize -> Add hydrogen -> OK -> OK
Or try the following Web servers:
http://bioserv.rpbs.univ-paris-diderot.fr/services/SolyPep/
http://bioware.ucd.ie/~cyclops/cgi-bin/webpep.cgi
hi, you can use pep-fold server at
http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3/
hi, you can use pep-fold server at
http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3/
Thanks you all for your help
I used I-Tasser web server and I get a model. But I'd like to try Chimera and pep-fold as Yoshinobu and Mokhtar suggested.
If I encounter problems I will come back to you.
Thanks
Abdo
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