Zhen‐Yu Chen

Sirui Liu, Jun Zhang, Haotian Chu et al.

Proteins are essential component of human life and their structures are important for function and mechanism analysis. Recent work has shown the potential of AI-driven methods for protein structure prediction. However, the development of new models is restricted by the lack of dataset and benchmark training procedure. To the best of our knowledge, the existing open source datasets are far less to satisfy the needs of modern protein sequence-structure related research. To solve this problem, we present the first million-level protein structure prediction dataset with high coverage and diversity, named as PSP. This dataset consists of 570k true structure sequences (10TB) and 745k complementary distillation sequences (15TB). We provide in addition the benchmark training procedure for SOTA protein structure prediction model on this dataset. We validate the utility of this dataset for training by participating CAMEO contest in which our model won the first place. We hope our PSP dataset together with the training benchmark can enable a broader community of AI/biology researchers for AI-driven protein related research.

Yueming Xu, Jiahui Zhang, Ze Huang et al.

Despite the impressive progress on understanding and generating images shown by the recent unified architectures, the integration of 3D tasks remains challenging and largely unexplored. In this paper, we introduce UniUGG, the first unified understanding and generation framework for 3D modalities. Our unified framework employs an LLM to comprehend and decode sentences and 3D representations. At its core, we propose a spatial decoder leveraging a latent diffusion model to generate high-quality 3D representations. This allows for the generation and imagination of 3D scenes based on a reference image and an arbitrary view transformation, while remaining supports for spatial visual question answering (VQA) tasks. Additionally, we propose a geometric-semantic learning strategy to pretrain the vision encoder. This design jointly captures the input's semantic and geometric cues, enhancing both spatial understanding and generation. Extensive experimental results demonstrate the superiority of our method in visual representation, spatial understanding, and 3D generation. The source code will be released upon paper acceptance.

Zicheng Ma, Chuanliu Fan, Zhicong Wang et al.

Large language models have made remarkable progress in the field of molecular science, particularly in understanding and generating functional small molecules. This success is largely attributed to the effectiveness of molecular tokenization strategies. In protein science, the amino acid sequence serves as the sole tokenizer for LLMs. However, many fundamental challenges in protein science are inherently structure-dependent. The absence of structure-aware tokens significantly limits the capabilities of LLMs for comprehensive biomolecular comprehension and multimodal generation. To address these challenges, we introduce a novel framework, ProtTeX, which tokenizes the protein sequences, structures, and textual information into a unified discrete space. This innovative approach enables joint training of the LLM exclusively through the Next-Token Prediction paradigm, facilitating multimodal protein reasoning and generation. ProtTeX enables general LLMs to perceive and process protein structures through sequential text input, leverage structural information as intermediate reasoning components, and generate or manipulate structures via sequential text output. Experiments demonstrate that our model achieves significant improvements in protein function prediction, outperforming the state-of-the-art domain expert model with a twofold increase in accuracy. Our framework enables high-quality conformational generation and customizable protein design. For the first time, we demonstrate that by adopting the standard training and inference pipelines from the LLM domain, ProtTeX empowers decoder-only LLMs to effectively address diverse spectrum of protein-related tasks.