1. A simple spatial extension to the extended connectivity interaction features for binding affinity prediction
- Author
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Orhobor, Oghenejokpeme I, Rehim, Abbi Abdel, Lou, Hang, Ni, Hao, King, Ross D, Orhobor, Oghenejokpeme I. [0000-0003-1178-611X], King, Ross D. [0000-0001-7208-4387], Apollo - University of Cambridge Repository, Orhobor, Oghenejokpeme I [0000-0003-1178-611X], King, Ross D [0000-0001-7208-4387], and King, Ross [0000-0001-7208-4387]
- Subjects
scoring functions ,protein binding affinity prediction ,Multidisciplinary ,machine learning ,Biochemistry, cellular and molecular biology ,Research articles - Abstract
Peer reviewed: True, 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.
- Published
- 2022
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