Can autodock vina differentiate between cis and trans isomer? Also which software can be used to generate cis and trans isomer of compounds in sdf ?

30 April 2025 1 5K Report

Iam trying to dock cis and trans isomer of certain compounds with a protein.

Yes, vina should be capable of differentiating between cis and trans isomers as well as other types of stereoisomers. Thd differentiation would depend upon there being signficiant differences in the protein-ligand interactions that determine the overall docking score. You can generate cis and trans isomers using OpenBabel and other software, such as ChemAxon MarvinSketch.

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