Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

By Zoe Cournia, Bryce K. Allen, Woody Sherman. Journal of Chemical Information and Modeling, 2017

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Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field (2023, neutral): “25,26 This process, known as computer-aided drug design (CADD), requires quantitatively accurate descriptions of many chemically diverse drug candidates, their interactions with different chemical moieties and accurate predictions of their physical properties in various environments.”
Best practices for constructing, preparing, and evaluating protein-ligand binding aﬃnity benchmarks [Article v0.2] (2021, background): “Binding free energy calculations—particularly alchemical binding free energy calculations—have emerged as arguably the most promising tool [6].”
Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0] (2021, background): “Binding free energy calculations—particularly alchemical binding free energy calculations—have emerged as arguably the most promising tool [6].”
Scalable molecular dynamics on CPU and GPU architectures with NAMD. (2020, neutral): “242 Supported by progress on the hardware front, most prominently, with the availability of fast GPUs on a variety of platforms, as well as on the software front, with optimally designed tools (see Secs.”