Hi everybody,
While learning to use the ChemAxon Reactor tool embedded in JChem (it’s the first time I try to use a chemoinformatic software so sorry if I do not express myself properly), I am experiencing some difficulties in performing in silico peptide cyclization reactions.
1) Starting from a list of amino acids I managed to obtain linear peptides by iteratively running the “Amide synthesis from carboxylic acids” reaction in combinatorial mode. Here I found the first difficulties, since I do not obtain all the possible combinations. Starting e.g. from Ala, Asp and Lys (as reagents), I obtain some of the possible di-peptides, while other ones are not present among the reaction products.
Analogously, some possible products are missing during subsequent elongation of peptides by reacting the obtained di-peptides with the starting amino acids.
How can I obtain all the possible combinations? What might be the problem?
2) Is it possible to perform peptide cyclization by reacting together either the terminal amino and carboxylic groups or by introducing some reactive groups at each end of the linear peptide? If so, what is the correct procedure to define a suitable cyclization reaction?
3) Once obtained a library of (cyclic) peptides is it possible to export each of them in a separate file with an extension readable by other tools (e.g. PDB files)? I mean, from an Instant Jchem grid view of a library, I managed to export a .sdf file containing all the molecular structures and to convert it to a .pdb file by MarvinSketch, but how to obtain a separate .pdb file for each molecule?
I would be very grateful if someone could help me.
Best regards.
Filippo.
Try using Pep-cyclizer. I am myself trying to design cyclic peptides in silico. I must warn you the user interface is confusing. I myself did not get any success with this.
https://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::PEP-Cyclizer Filippo Vascon
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