I was wondering if there's some service similar to ZINC but where you can download virtual libraries (some thousands) of short peptides (3-5, maybe 6 residues) instead of small molecules, to use for virtual screening.
Thanks all
Not sure such libraries exist. Peptides are usually made to order. And it is so easy to enumerate a peptide library of any size either using a commercial software, such as Pipeline Pilot (3dsbiovia.com) or a public one -- https://www.knime.com/knime-applications/chemical-library-enumeration.
Hi Davide,
I recommend the following web servers and software;
(1) SolyPep is a fast and flexible random sequence generator for producing peptides selected for their aqueous solubility,
http://bioserv.rpbs.univ-paris-diderot.fr/services/SolyPep/
(2) PEP-FOLD is a de novo approach aimed at predicting peptide structures from amino acid sequences,
http://bioserv.rpbs.univ-paris-diderot.fr/services/SolyPep/
(3) CycloPs is a cyclic peptide library generator,
https://github.com/fergaljd/cyclops
Article CycloPs: Generating Virtual Libraries of Cyclized and Constr...
Thanks a lot for your answers guys. Generating peptide structures for virtual screening is sometimes tricky and often a long task. I've developed a modeller-based automatic peptide structure generator for a pilot VS study and, although it was a mixed bash python script, it worked quite good by producing good structures and employed the capability of modeller to build structures with modified aminoacids. However, since it runs on our machines, it suffers of hardware (disk space and cpu) limitation and for this reason, according to my opinion, it would be more desirable an external database by which it could be possible to download all the peptide structures you need. Have you guys ever worked on virtual screening of very small peptides or cyclopeptides?