Predicting the binding of small molecules to proteins through invariant representation of the molecular structure

R. Beccaria; A. Lazzeri; G. Tiana

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arXiv · 2405.04916

Predicting the binding of small molecules to proteins through invariant representation of the molecular structure

R. Beccaria·A. Lazzeri·G. Tiana

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Abstract

We present a computational scheme for predicting the ligands that bind to a pocket of known structure. It is based on the generation of a general abstract representation of the molecules, which is invariant to rotations, translations and permutations of atoms, and has some degree of isometry with the space of conformations. We use these representations to train a non-deep machine learning algorithm to classify the binding between pockets and molecule pairs, and show that this approach has a better generalization capability than existing methods.

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R. Beccaria, A. Lazzeri, G. Tiana. 2024-05-08. Predicting the binding of small molecules to proteins through invariant representation of the molecular structure. https://arxiv.org/abs/2405.04916

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