RINRUS: A Toolkit for the Construction of Reproducible and Reliable QM-Cluster Models of Enzyme Active Sites

Abstract

Effectively constructing an enzyme active site model is not only the most important task involved in quantum mechanical (QM) modeling of enzymes; it is also one of the most difficult. Without widely agreed-upon standards for selecting, truncating, and constraining residues, QM-cluster models have traditionally been built by bespoke approaches that are rarely consistent between labs. The Residue Interaction Network ResidUe Selector (RINRUS) is a software toolkit that automates and standardizes QM-cluster model construction with clear rules guaranteeing predictability and reproducibility. By selecting active site residues with interatomic contact networks, RINRUS replaces tedious visual inspection and chemical intuition with a data-driven approach. Algorithmic protocols are used for structure trimming, capping, and constraining to ensure the protein is truncated in chemically sensible places while keeping the system size reasonable. RINRUS can also prepare QM input files for the Gaussian, ORCA, Q-Chem, and Psi4 software packages. This fast and user-friendly automation of QM-cluster model design and input file preparation eliminates many of the learning barriers, hidden labor costs of project design/implementation, and inconsistencies that have historically plagued QM-cluster modeling. RINRUS is open-source and available for download at https://github.com/natedey/RINRUS.

Publication Title

Wiley Interdisciplinary Reviews Computational Molecular Science

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