KinForm: kinetics-informed feature optimised representation models for enzyme kcat and KM prediction

Kinetic parameters such as the turnover number (k_cat) and Michaelis constant (K_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 Modelling Cambrian, Evolutionary Scale Modelling 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.