Using bio/cheminformatics in atomistic quantum mechanical enzyme simulations

Abstract

Enzyme simulations are notoriously challenging as their large size prevents modeling the whole enzyme with highly accurate but computationally expensive quantum mechanical (QM) methods. Currently, only the chemically important “active site” residues/substrates/cofactors are modeled with QM-cluster or QM/MM methods. However, determining which biological sub-units necessarily should be included in the QM region remains ambiguous. Current practices for model construction typically suffer from human bias and unclear methodology.