Accurate identification of protein active sites at the residue level is crucial for understanding protein function and advancing drug discovery. However, current methods face two critical challenges: vulnerability in single-instance prediction due to sparse training data, and inadequate modality reliability estimation that leads to performance degradation when unreliable modalities dominate fusion processes. To address these challenges, we introduce Multimodal Mixtureof-Experts with Retrieval Augmentation (MERA), the first retrieval-augmented framework for protein active site identification. MERA employs hierarchical multi-expert retrieval that dynamically aggregates contextual information from chain, sequence, and active-site perspectives through residuelevel mixture-of-experts gating. To prevent modality degradation, we propose a reliability-aware fusion strategy based on Dempster–Shafer evidence theory that quantifies modality trustworthiness through belief mass functions and learnable discounting coefficients, enabling principled multimodal integration. Extensive experiments on ProTAD-Gen and TS125 datasets demonstrate that MERA achieves state-of-the-art performance, with 90% AUPRC on active site prediction and significant gains on peptide-binding site identification, validating the effectiveness of retrieval-augmented multi-expert modeling and reliability-guided fusion

MOTIVATION: Traditional drug discovery methods are costly and inefficient, while existing deep learning approaches remain limited by task specificity and practical applicability. Accurately modeling protein-molecule interactions is critical for advancing virtual screening, docking, and drug design. RESULTS: We propose DrugBLIP, a multi-task graph transformer model based on SE(3)-equivariant architectures, to unify protein-molecule interaction learning. By integrating contrastive learning, matching tasks, and docking optimization, DrugBLIP captures 3D spatial relationships through a hybrid graph transformer framework. Evaluations demonstrate state-of-the-art performance: DrugBLIP achieves an AUROC of 0.8217 and BEDROC of 0.5743 on virtual screening, outperforming traditional and deep learning baselines by 10%-127% across metrics. It also attains 91.2% top-1 docking success on CASF-2016 and 41.8% target fishing accuracy, showcasing robustness in diverse scenarios. Additionally, DrugBLIP reduces computational time by 700× compared to traditional docking tools. AVAILABILITY AND IMPLEMENTATION: Code is available at https://github.com/Wolkenwandler/DrugBLIP and archived at Zenodo with DOI: 10.5281/zenodo.16990700.

Immunoglobulins are crucial proteins produced by the immune system to identify and bind to foreign substances, playing an essential role in shielding organisms from infections and diseases. Designing specific antibodies opens new pathways for disease treatment. With the rise of deep learning, AI-driven drug design has become possible, leading to several methods for antibody design. However, many of these approaches require additional conditions that differ from real-world scenarios, making it challenging to incorporate them into existing antibody design processes. Here, we introduce IgGM, a generative model for the de novo design of immunoglobulins with functional specificity. IgGM simultaneously generates antibody sequences and structures for a given antigen, consisting of three core components: a pre-trained language model for extracting sequence features, a feature learning module for identifying pertinent features, and a prediction module that outputs designed antibody sequences and the predicted complete antibody-antigen complex structure. IgGM effectively predicts structures and designs novel antibodies and nanobodies. This makes it highly applicable in a wide range of practical situations related to antibody and nanobody design. Code is available at: https://github.com/TencentAI4S/IgGM.

With the development of biotechnology, RNA therapies have shown great potential. However, different from proteins, the sequences corresponding to a single RNA three-dimensional structure are more abundant. Most of the existing RNA design methods merely take into account the secondary structure of RNA, or are only capable of generating a limited number of candidate sequences. To address these limitations, we propose a geometric-algebra-enhanced $\textbf{B}$ayesian $\textbf{F}$low $\textbf{N}$etwork for the inverse design of $\textbf{R}$NA, called $\textbf{RBFN}$. RBFN uses a Bayesian Flow Network to model the distribution of nucleotide sequences in RNA, enabling the generation of more reasonable RNA sequences. Meanwhile, considering the more flexible characteristics of RNA conformations, we utilize geometric algebra to enhance the modeling ability of the RNA three-dimensional structure, facilitating a better understanding of RNA structural properties. In addition, due to the scarcity of RNA structures and the limitation that there are only four types of nucleic acids, we propose a new time-step distribution sampling to address the scarcity of RNA structure data and the relatively small number of nucleic acid types. Evaluation on the single-state fixed-backbone re-design benchmark and multi-state fixed-backbone benchmark indicates that RBFN can outperform existing RNA design methods in various RNA design tasks, enabling effective RNA sequence design.

Unsupervised domain adaptation person re-identification (UDA person re-ID) aims at transferring the knowledge on the source domain with expensive manual annotation to the unlabeled target domain. Most of the recent papers leverage pseudo-labels for the target images to accomplish this task. However, the noise in the generated labels hinders the identification system from learning discriminative features. To address this problem, we propose a deep mutual distillation (DMD) to generate reliable pseudo-labels for UDA person re-ID. The proposed DMD applies two parallel branches for feature extraction, and each branch serves as the teacher of the other to generate pseudo-labels for its training. This mutually reinforcing optimization framework enhances the reliability of pseudo-labels, improving the identification performance. In addition, we present a bilateral graph representation (BGR) to describe the pedestrian images. BGR mimics the person re-identification of the human to aggregate the identity features according to the visual similarity and attribute consistency. Experimental results on Market-1501 and Duke demonstrate the effectiveness and generalization of the proposed method.