Supplementary material for 'Binding free energies for the SAMPL8 CB8 "Drugs of Abuse" challenge from umbrella sampling combined with Hamiltonian replica exchange'

Binding affinities of seven drug molecules (G1-G7) towards a common receptor (cucurbit[8]uril, CB8) were estimated from molecular dynamics (MD) simulations in the scope of the recent SAMPL8 CB8 "Drugs of Abuse" challenge using the GROMACS MD package. To compare with experimental data, a scheme for correcting the raw simulation estimates was proposed in the related publication on the basis of five training molecules (GT1-GT5) with experimentally known binding affinities towards CB8. The deposited dataset contains coordinates and molecular topologies in GROMACS format as well as free energy profiles accompanying the related publication. For each guest molecule, two protonation states were simulated (protonated, deprotonated) and for one of the drugs, G5, both of its enantiomeric forms (R, S) were considered.

本数据集基于近期SAMPL8 CB8“滥用药物”挑战赛的研究框架，采用GROMACS分子动力学（Molecular Dynamics，MD）软件包，通过分子动力学模拟估算了7种药物分子（G1~G7）与通用受体葫芦[8]脲（cucurbit[8]uril，CB8）的结合亲和力。为与实验数据比对，相关研究以5种已明确CB8结合亲和力的训练分子（GT1~GT5）为依据，提出了针对原始模拟估算值的校正方案。本存档数据集包含GROMACS格式的坐标文件与分子拓扑文件，以及配套相关研究发表的自由能分布曲线。针对每种客体分子，本研究均模拟了两种质子化状态（质子化态、去质子化态）；其中针对药物分子G5，还同时考虑了其两种对映异构体（R型、S型）。