Abstract Motivation Cytochromes P450 are the most important class of drug metabolizing enzymes. Prediction of drug metabolism is important in development of new drugs, to understand and reduce adverse drug reactions and to reduce animal testing. Results SMARTCyp 3.0 is an updated version of our previous web server for prediction of site-of-metabolism for Cytochrome P450-mediated metabolism, now in Python 3 with increased structural coverage and new features. The SMARTCyp program is a first principle-based method using density functional theory determined activation energies for more than 250 molecules to identify the most likely site-of-metabolism. New features include a similarity measure between the query molecule and the model fragment, a new graphical interface and additional parameters expanding the structural coverage of the SMARTCyp program. Availability and implementation The SMARTCyp server is freely available for use on the web at smartcyp.sund.ku.dk. Supplementary information Supplementary data are available at Bioinformatics online.