I want to perform a fragment based virtual screening using some vendors' databases. Nevertheless, some databases may not be downloaded in the desired protonation state.
Once there are more than 5k fragments, it is not viable to make an individual analysis. So I hope that you could help with this issue.
Thanks in advance,
Renan Gomes
Hi Renan,
Try Open Babel with -p option:
https://openbabel.org/wiki/Tutorial:Basic_Usage
Hii..
There are number of software’s available like:
LIGPREP (add hydrogen atoms, generate up to eight different tautomers, stereoisomers, and change the ionization state of the molecule according to a given pH value).
PROTONATE 3D (adds hydrogen atoms, produce rotamers, tautomers and determines accurate protonation for polar groups using a free energy optimization)
Openbabel and I-interpret (softwares developed for the file format conversion and add hydrogen atoms)
Please read the attached link
https://pubs.acs.org/doi/full/10.1021/ci800420z?src=recsys
Regards
Anu
You can use chemaxon which has an academic license or MOE that has an educational license. I recommend ChemAxon, this has GUI, shows all the compounds in 2D or 3D, determines the protonation states from a tritiation curve and populations of microstates of the compounds. MOE is also very good and has about 100 molecular descriptors that could be useful in your later work. Both programs have the option of determining the protonation states of chemical compounds. Sorry for the language problems. Best regard
