HAIRpred2: Human Host-Specific Prediction of Antibody-Interacting Residues Using Hybrid Physicochemical and Structural Features

Abstract

1.Prediction of conformational B-cell epitopes is critical for vaccine design, immunotherapy, and antibody engineering. To date, several host-independent computational methods have been developed for predicting antibody-interacting residues in antigen structures. However, it is well established that antigen-antibody (Ag-Ab) interactions vary depending on the host immune system indicating the importance of developing host-specific prediction models. In this study, we present, for the first time, a human host-specific method, HAIRpred2, that predicts antibody-interacting residues in an antigen from its tertiary structure. The dataset was derived from HAIRpred and comprises 277 human Ag-Ab complexes, with 221 structures used for training and 56 for independent testing. Preliminary analysis revealed that residues with a relative surface accessibility (RSA) below 0.05, corresponding to buried regions, are highly likely to be non-interacting, underscoring the importance of structural accessibility in antibody recognition. To identify the most informative features, we evaluated multiple feature representations, including RSA, large language model (LLM)-based embeddings, distance-based features, and physicochemical properties. A model trained on single-residue RSA features achieved an AUC of 0.72. Incorporating a sliding window of 15 residues to capture local structural context improved performance to an AUC of 0.75. The best performance (AUC = 0.78 on the independent test set) was achieved by integrating RSA with physicochemical descriptors. Benchmarking against existing antibody-interaction prediction methods on the same independent dataset demonstrated that HAIRpred2 outperforms current tools, further highlighting the advantage of host-specific modeling. HAIRpred2 is freely available as a web server at https://webs.iiitd.edu.in/raghava/hairpred2/. HighlightsO_LIDevelopment of HAIRpred2, the first human host-specific method for predicting antibody-interacting residues. C_LIO_LIAnalysis of 277 human antigen-antibody complexes to capture host-dependent interaction patterns. C_LIO_LIRelative surface accessibility (RSA) identified as a key determinant, with buried residues rarely participating in interactions. C_LIO_LIIntegration of RSA with physicochemical features achieved the best performance (AUC = 0.78) on an independent dataset. C_LIO_LIHAIRpred2 outperforms existing methods and is available as a web server for epitope prediction. C_LI