A Benchmark Test of High-Throughput Atomistic Modeling for Octa-Acid Host–Guest Complexes

Abstract

Years of massive applications of high-throughput atomistic modeling tools such as molecular docking and end-point free energy calculations in the drug industry and academic exploration have made them indispensable parts of hierarchical screening. While the similarities between host–guest and protein–ligand complexes lead to the direct extension of techniques for protein–ligand screening to host–guest systems, the practical performance of these hit identification tools remains unclear in host-–-guest binding. Recent reports on specific host–guest complexes suggest that the experience on the accuracy ladder accumulated from protein–ligand cases could be invalid in host–guest complexes, which makes it an urgent need to perform a systematic benchmark to secure solid numerical supports and guidance of practical setups. Concerning molecular docking, there still lacks a comprehensive benchmark considering popular docking programs. As for end-point reranking, quantitative and rigorous free energy estimation via end-point formulism requires establishing statistically meaningful measurements of uncertainties due to finite sampling, which is neglected or underestimated by a significant portion in almost all main-stream applications. Further, a face-to-face comparison between different screening tools is required for the design of a hierarchical workflow. To fill the above-mentioned critical gaps, in this work, using a dataset containing tens of host–guest complexes involving basket-like macromolecular hosts from the octa acid family, we extensively benchmark seven academic docking protocols and perform post-docking end-point rescoring with twenty protocols. The resulting comprehensive benchmark provides conclusive pictures of the practical value of docking and end-point screening in OA host–guest binding.