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Literature DB >> 27480697

The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP.

Yuan Hu¹, Brad Sherborne², Tai-Sung Lee³, David A Case³, Darrin M York⁴, Zhuyan Guo⁵.

Abstract

In drug discovery, protonation states and tautomerization are easily overlooked. Through a Merck-Rutgers collaboration, this paper re-examined the initial settings and preparations for the Thermodynamic Integration (TI) calculation in AMBER Free-Energy Workflows, demonstrating the value of careful consideration of ligand protonation and tautomer state. Finally, promising results comparing AMBER TI and Schrödinger FEP+ are shown that should encourage others to explore the value of TI in routine Structure-based Drug Design.

Entities: Chemical Disease Mutation Species

Keywords: Free energy calculation; Free energy perturbation; Protein–ligand binding affinity; Protonation; Tautomerization; Thermodynamic integration

Mesh：

Substances：

Year: 2016 PMID： 27480697 PMCID： PMC6360336 DOI： 10.1007/s10822-016-9920-5

Source DB: PubMed Journal: J Comput Aided Mol Des ISSN： 0920-654X Impact factor: 3.686

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