Cross-Gate MLP with Protein Complex Invariant Embedding is A One-Shot Antibody Designer

TL;DR

This paper introduces a novel one-shot model for antibody CDR design that combines geometric protein complex modeling with sequence-structure co-learning, outperforming existing methods in efficiency and accuracy.

Contribution

It proposes a simple, effective approach that decouples geometric modeling from sequence-structure co-learning, utilizing a protein complex invariant embedding and cross-gate MLP for antibody design.

Findings

Achieves superior performance over state-of-the-art methods

Enables one-shot design of antibody CDRs

Effectively models protein complex geometry

Abstract

Antibodies are crucial proteins produced by the immune system in response to foreign substances or antigens. The specificity of an antibody is determined by its complementarity-determining regions (CDRs), which are located in the variable domains of the antibody chains and form the antigen-binding site. Previous studies have utilized complex techniques to generate CDRs, but they suffer from inadequate geometric modeling. Moreover, the common iterative refinement strategies lead to an inefficient inference. In this paper, we propose a \textit{simple yet effective} model that can co-design 1D sequences and 3D structures of CDRs in a one-shot manner. To achieve this, we decouple the antibody CDR design problem into two stages: (i) geometric modeling of protein complex structures and (ii) sequence-structure co-learning. We develop a novel macromolecular structure invariant embedding, typically for protein complexes, that captures both intra- and inter-component interactions among the backbone atoms, including C$\alpha$, N, C, and O atoms, to achieve comprehensive geometric modeling. Then, we introduce a simple cross-gate MLP for sequence-structure co-learning, allowing sequence and structure representations to implicitly refine each other. This enables our model to design desired sequences and structures in a one-shot manner. Extensive experiments are conducted to evaluate our results at both the sequence and structure levels, which demonstrate that our model achieves superior performance compared to the state-of-the-art antibody CDR design methods.