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. 2022 Mar 11;13:837715. doi: 10.3389/fphar.2022.837715

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Copyright © 2022 Shi, Singha, Srivastava, Pu, Ramanujam and Brylinski.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Flowchart of the evaluation by pocket structure alignments. For a target pocket (A), a molecule is generated by Pocket2Drug (B). This compound is then scanned through the PubChem BioAssay for similar molecules for which experimental complex structures are available in the Protein Data Bank. The extracted binding site (C) corresponding to the know interaction in PubChem BioAssay is structurally aligned to the target pocket by PocketAlign. A high-quality alignment (D) indicates that the generated molecule is likely to bind to the target pocket.