KinForm: Kinetics Informed Feature Optimised Representation Models for Enzyme $k_{cat}$ and $K_{M}$ Prediction

• URL: http://arxiv.org/abs/2507.14639v1
• Date: Sat, 19 Jul 2025 14:34:57 GMT
• Title: KinForm: Kinetics Informed Feature Optimised Representation Models for Enzyme $k_{cat}$ and $K_{M}$ Prediction
• Authors: Saleh Alwer, Ronan Fleming,
• Abstract summary: KinForm is a machine learning framework designed to improve predictive accuracy and generalisation for kinetic parameters.<n>We observe improvements from binding-site probability pooling, intermediate-layer selection, PCA, and oversampling of low-identity proteins.
• Score: 0.0
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Kinetic parameters such as the turnover number ($k_{cat}$) and Michaelis constant ($K_{\mathrm{M}}$) are essential for modelling enzymatic activity but experimental data remains limited in scale and diversity. Previous methods for predicting enzyme kinetics typically use mean-pooled residue embeddings from a single protein language model to represent the protein. We present KinForm, a machine learning framework designed to improve predictive accuracy and generalisation for kinetic parameters by optimising protein feature representations. KinForm combines several residue-level embeddings (Evolutionary Scale Modeling Cambrian, Evolutionary Scale Modeling 2, and ProtT5-XL-UniRef50), taken from empirically selected intermediate transformer layers and applies weighted pooling based on per-residue binding-site probability. To counter the resulting high dimensionality, we apply dimensionality reduction using principal--component analysis (PCA) on concatenated protein features, and rebalance the training data via a similarity-based oversampling strategy. KinForm outperforms baseline methods on two benchmark datasets. Improvements are most pronounced in low sequence similarity bins. We observe improvements from binding-site probability pooling, intermediate-layer selection, PCA, and oversampling of low-identity proteins. We also find that removing sequence overlap between folds provides a more realistic evaluation of generalisation and should be the standard over random splitting when benchmarking kinetic prediction models.

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