Antibody Complementarity Determining Regions (CDRs) design using Constrained Energy Model

Abstract

In recent years, therapeutic antibodies have become one of the fastest-growing classes of drugs and have been approved for the treatment of a wide range of indications, from cancer to autoimmune diseases. Complementarity-determining regions (CDRs) are part of the variable chains in antibodies and determine specific antibody-antigen binding. Some explorations use in silicon methods to design antibody CDR loops. However, the existing methods faced the challenges of maintaining the specific geometry shape of the CDR loops. This paper proposes a Constrained Energy Model (CEM) to address this issue. Specifically, we design a constrained manifold to characterize the geometry constraints of the CDR loops. Then we design the energy model in the constrained manifold and only depict the energy landscape of the manifold instead of the whole space in the vanilla energy model. The geometry shape of the generated CDR loops is automatically preserved. Theoretical analysis shows that learning on the constrained manifold requires less sample complexity than the unconstrained method. CEM's superiority is validated via thorough empirical studies, achieving consistent and significant improvement with up to 33.4% relative reduction in terms of 3D geometry error (Root Mean Square Deviation, RMSD) and 8.4% relative reduction in terms of amino acid sequence metric (perplexity) compared to the best baseline method. The code is publicly available at https://github.com/futianfan/energy-model4antibody-design