Fig. 5: A two-layer framework considering environmental factors.
From: UniKP: a unified framework for the prediction of enzyme kinetic parameters
a A two-layer framework called EF-UniKP that consists of a base layer and a meta layer. The base layer contains two models, namely UniKP and Revised UniKP. The UniKP takes the concatenated representation vector of the enzyme and substrate as input, while the Revised UniKP uses a concatenated representation vector of the enzyme and substrate, combined with the pH or temperature value. Both models are trained using the Extra Trees algorithm. The meta layer of this framework includes a linear regressor that uses the predicted kcat values from both the UniKP and Revised UniKP to predict the final kcat value. Scatter plot illustrating the Pearson coefficient correlation (PCC) between experimentally measured kcat values and predicted kcat values of Revised UniKP for pH set (b) (N = 636) and temperature set (c) (N = 572). The color gradient represents the density of data points, ranging from blue (0.02) to red (0.28). d Coefficient of determination (R2) values between experimentally measured kcat values and predicted kcat values on pH and temperature test sets of EF-UniKP, Revised UniKP and UniKP. Light bars represent R2 of EF-UniKP, dark bars for Revised UniKP and darkish bars for UniKP. e R2 values between experimentally measured kcat values and predicted kcat values on more strict pH and temperature test sets of EF-UniKP, Revised UniKP and UniKP. These are the samples in the test set where at least either the substrate or enzyme was not included in the training set, resulting in 62 and 61 samples for pH and temperature, respectively. Light bars represent R2 of EF-UniKP, dark bars for Revised UniKP and darkish bars for UniKP. Source data are provided as a Source Data file.
