Can We Automate Computational Studies of Enzymes? Lessons from Small-Molecule Studies

This document discusses the potential for automating computational studies of enzymes based on lessons from studies of small molecule combustion and atmospheric chemistry. It notes that catalytic mechanisms can now be automatically extracted from reaction networks and that semiempirical quantum mechanics methods may allow automated conformational sampling and reaction setup for enzymes, though their accuracy needs testing. Tools developed so far in the author's group include methods for automatically extracting elementary steps from reaction networks and databases of enzyme reaction energies and barriers calculated at different levels of theory.