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Decision Making in Structure-Based Drug Discovery: Visual Inspection of Docking Results

Cite this: J. Med. Chem. 2021, 64, 5, 2489–2500
Publication Date (Web):February 22, 2021
https://doi.org/10.1021/acs.jmedchem.0c02227
Copyright © 2021 American Chemical Society

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    Abstract

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    Molecular docking is a computational method widely used in drug discovery. Due to the inherent inaccuracies of molecular docking, visual inspection of binding modes is a crucial routine in the decision making process of computational medicinal chemists. Despite its apparent importance for medicinal chemistry projects, guidelines for the visual docking pose assessment have been hardly discussed in the literature. Here, we review the medicinal chemistry literature with the aim of identifying consistent principles for visual inspection, highlighting cases of its successful application, and discussing its limitations. In this context, we conducted a survey reaching experts in both academia and the pharmaceutical industry, which also included a challenge to distinguish native from incorrect poses. We were able to collect 93 expert opinions that offer valuable insights into visually supported decision-making processes. This perspective shall motivate discussions among experienced computational medicinal chemists and guide young scientists new to the field to stratify their compounds.

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