Protein-protein interactions (PPIs) are governed by surface complementarity and hydrophobic interactions at protein interfaces. However, designing diverse and physically realistic protein structure and surfaces that precisely complement target receptors remains a significant challenge in computational protein design. In this work, we introduce PepBridge, a novel framework for the joint design of protein surface and structure that seamlessly integrates receptor surface geometry and biochemical properties. Starting with a receptor surface represented as a 3D point cloud, PepBridge generates complete protein structures through a multi-step process. First, it employs denoising diffusion bridge models (DDBMs) to map receptor surfaces to ligand surfaces. Next, a multi-model diffusion model predicts the corresponding structure, while Shape-Frame Matching Networks ensure alignment between surface geometry and backbone architecture. This integrated approach facilitates surface complementarity, conformational stability, and chemical feasibility. Extensive validation across diverse protein design scenarios demonstrates PepBridge's efficacy in generating structurally viable proteins, representing a significant advancement in the joint design of top-down protein structure.

Data imputation is a crucial task due to the widespread occurrence of missing data. Many methods adopt a two-step approach: initially crafting a preliminary imputation (the "draft") and then refining it to produce the final missing data imputation result, commonly referred to as "draft-then-refine". In our study, we examine this prevalent strategy through the lens of graph Dirichlet energy. We observe that a basic "draft"imputation tends to decrease the Dirichlet energy. Therefore, a subsequent "refine"step is necessary to restore the overall energy balance. Existing refinement techniques, such as the Graph Convolutional Network (GCN), often result in further energy reduction. To address this, we introduce a new framework, the Graph Laplacian Pyramid Network (GLPN). GLPN incorporates a U-shaped autoencoder and residual networks to capture both global and local details effectively. Through extensive experiments on multiple real-world datasets, GLPN consistently outperforms state-of-the-art methods across three different missing data mechanisms. The code is available at https://github.com/liguanlue/GLPN.