OpenFF 2.3.0rc1 Relative Binding Free Energy Benchmarks
收藏Zenodo2025-09-18 更新2026-05-26 收录
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https://zenodo.org/doi/10.5281/zenodo.17155666
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资源简介：
Overview
Relative binding free energy benchmarks of the openff-2.3.0rc1 release using the JACS set from (https://github.com/OpenFreeEnergy/IndustryBenchmarks2024).
Contents
Benchmark variants
The following benchmark variants were run: * `openff-2.3.0rc1_elf10`: simulations using OpenFF 2.3.0rc1 and AM1BCCELF10 charges using the OpenEye Toolkit. * `openff-2.3.0rc1_nagl`: simulations using OpenFF 2.3.0rc1 and AshGC v0.1rc3 charges
RBFE data
The `data` folder contains all the ddG data for each transformation in each set. These are stored as TSV files within subdirectories for each system in the JACS set.
Plots
dG (MLE-derived using cinnabar) and ddG plots are present for each system under the `plots` folder.
Simulation details
* All simulations were carried out using the RelativeHybridTopology protocol in OpenFE v1.4.* Mappings were created using Kartograf, these are the same as those used in the OpenFE industry benchmarks.* Transformation edges were created using Lomap, these are the same as those used in the OpenFE industry benchmarks.* Simulations used openfe default settings, except the following: * Dodecahedron solvent box with 1 nm padding in complex and 1.5 nm padding in solvent * 2.5 ps HREX exchange rate * 0.9 nm short range interaction cutoff
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Zenodo创建时间：
2025-09-18
