Hi @all !!!
I have used mcule data base by structure-based virtual screening aginst target receptor. I have down loaded smile file and tried to genrate mole2 file using USCF chimera by adding hydrogen bonds and energy minimization (as I think at the stage of file conversion have any problem) but facing problem while molecular docking using swiss dock or other online docking web based servers. Kindly guide me, how to generate 2D or 3D structure of ligand and convert smiles into mole2 format.
Thanks in Advance
Regards
Farman Ali
You have several options available. Open Babel is one of the most used (http://openbabel.org/wiki/Main_Page); You can also use MOE (Requires license https://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm) and ChemAxon (https://chemaxon.com/). The latter has an academic license and is the one I recommend. ChemAxon reads the database in the supported formats (smi, sdf, etc) and allows to convert them to other formats (mol, mol2, pdb, sdf, etc), generate 3D structures, protonate assign partial charge, among other functions.
Best wishes
Hi Farman,
To build 3D models from 2D smile files, try Frog 2 server:
http://mobyle.rpbs.univ-paris-diderot.fr/cgi-bin/portal.py#forms::Frog2
Paste the canonical smiles string of interest here
https://cactus.nci.nih.gov/translate/
Translate to pdb format and save the pdb file.
Using OpenBabelGUI software, covert the saved pdb file to mol2 format.
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