The SAMPL9 Host-Guest Blind Challenge: An Overview of Binding Free Energy Predictive Accuracy

02 November 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


We report the results of the SAMPL9 host-guest blind challenge for predicting binding free energies. The challenge focused on macrocycles from pillar[n]-arene and cyclodextrin host families, including WP6, and bCD and HbCD. A variety of methods were used by participants to submit binding free energy predictions. A machine learning approach based on molecular descriptors achieved the highest accuracy (RMSE of 2.04 kcal/mol) among ranked methods in the WP6 dataset. Interestingly, predictions for WP6 obtained via docking tended to outperform all methods (RMSE of 1.70 kcal/mol), most of which are MD based and computationally more expensive. In general, methods applying force fields achieved better correlation with experiments for WP6 opposed to the machine learning and docking models. In the cyclodextrin-phenothiazine challenge, the ATM approach emerged as the top performing method with RMSE less than 1.86 kcal/mol. Correlation metrics of ranked methods in this dataset was relatively poor compared to WP6. We also highlight several lessons learned to guide future work and help improve studies on the systems discussed. For example, WP6 may be present in other microstates other than its -12 state in the presence of certain guests. Machine learning approaches can be used to fine tune or help train force fields for certain chemistry (i.e WP6-G4). Certain phenothiazines occupy distinct primary and secondary orientations, some of which were considered individually for accurate binding free energies. The accuracy of predictions from certain methods while starting from a single binding pose/orientation demonstrate the sensitivity of calculated binding free energies to the orientation, and in some cases the likely dominant orientation for the system. Computational and experimental results suggest that guests phenothiazine core traverses both secondary and primary faces of the cyclodextrin hosts, bulky catioinic side chain will primarily occupy the primary face, and the phenothiazine core substituent resides at the larger secondary face.


host-guest binding
binding free energy
blind challenge

Supplementary materials

Supplementary Information
Additional figures and tables referenced in the manuscript.
SAMPL9 Host-guest supplementary GitHub document
Archive copy (10/23/27) of the SAMPL9 host-guest challenge GitHub repository. Contains directories for datasets, submission files, script(s) for analysis, challenge statistics data, plots and tables, and experimental data.

Supplementary weblinks


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