Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0]

@article{Hahn2022BestPF,
  title={Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0]},
  author={David F. Hahn and Christopher I. Bayly and Melissa L Boby and Hannah E. Bruce Macdonald and John D. Chodera and Vytautas Gapsys and Antonia Mey and David L. Mobley and Laura Perez Benito and Christina E. M. Schindler and Gary Tresadern and Gregory L. Warren},
  journal={Living Journal of Computational Molecular Science},
  year={2022}
}
1Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium; 2OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508 USA; 3Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA; 4MSD, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom; 5EaStCHEM School of Chemistry, David Brewster Road, Joseph Black Building, The King’s Buildings… 
4 Citations

Precise Binding Free Energy Calculations for Multiple Molecules Using an Optimal Measurement Network of Pairwise Differences.

TLDR
This work presents a computational method that substantially improves the statistical precision in BFE calculations for a set of ligands binding to a common receptor by dynamically allocating computational resources to different B FE calculations according to an optimality objective established in a previous work from this group and extended in this work.

Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.

TLDR
This initial Parsley force field affords accuracy similar to that of other general force fields when used to calculate relative binding free energies spanning 199 protein-ligand systems, and the resulting infrastructure allows us to rapidly optimize an entirely new force field with minimal human intervention.

Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design

TLDR
It is demonstrated that workflows built on open source software packages can efficiently leverage pre-exascale computing resources to screen hundreds of compounds in a matter of days.

Chemical Space Exploration with Active Learning and Alchemical Free Energies.

TLDR
This work explores how an active learning protocol can be combined with first-principles based alchemical free energy calculations to identify high affinity phosphodiesterase 2 (PDE2) inhibitors.

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