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Updated: Sep 23, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
A simple spatial extension to the extended connectivity interaction features for binding affinity prediction
Oghenejokpeme I Orhobor1, Abbi Abdel Rehim1, Hang Lou2
1Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK.
Abstract:
The representation of the protein-ligand complexes used in building machine learning models play an important role in the accuracy of binding affinity prediction. The Extended Connectivity Interaction Features (ECIF) is one such representation. We report that (i) including the discretized distances between protein-ligand atom pairs in the ECIF scheme improves predictive accuracy, and (ii) in an evaluation using gradient boosted trees, we found that the resampling method used in selecting the best hyperparameters has a strong effect on predictive performance, especially for benchmarking purposes.
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