Xiaoyong Pan

Xiao-Yu Guo, Yi-Fan Li, Yuan Liu et al.

Protein design has become a critical method in advancing significant potential for various applications such as drug development and enzyme engineering. However, protein design methods utilizing large language models with solely pretraining and fine-tuning struggle to capture relationships in multi-modal protein data. To address this, we propose ProtDAT, a de novo fine-grained framework capable of designing proteins from any descriptive protein text input. ProtDAT builds upon the inherent characteristics of protein data to unify sequences and text as a cohesive whole rather than separate entities. It leverages an innovative multi-modal cross-attention, integrating protein sequences and textual information for a foundational level and seamless integration. Experimental results demonstrate that ProtDAT achieves the state-of-the-art performance in protein sequence generation, excelling in rationality, functionality, structural similarity, and validity. On 20,000 text-sequence pairs from Swiss-Prot, it improves pLDDT by 6%, TM-score by 0.26, and reduces RMSD by 1.2 Å, highlighting its potential to advance protein design.

Ziqi Zhang, Shiheng Chen, Runze Yang et al.

Developing enzymes with desired thermal properties is crucial for a wide range of industrial and research applications, and determining temperature stability is an essential step in this process. Experimental determination of thermal parameters is labor-intensive, time-consuming, and costly. Moreover, existing computational approaches are often hindered by limited data availability and imbalanced distributions. To address these challenges, we introduce a curated temperature stability dataset designed for model development and benchmarking in enzyme thermal modeling. Leveraging this dataset, we present the \textit{Segment Transformer}, a novel deep learning framework that enables efficient and accurate prediction of enzyme temperature stability. The model achieves state-of-the-art performance with an RMSE of 24.03, MAE of 18.09, and Pearson and Spearman correlations of 0.33, respectively. These results highlight the effectiveness of incorporating segment-level representations, grounded in the biological observation that different regions of a protein sequence contribute unequally to thermal behavior. As a proof of concept, we applied the Segment Transformer to guide the engineering of a cutinase enzyme. Experimental validation demonstrated a 1.64-fold improvement in relative activity following heat treatment, achieved through only 17 mutations and without compromising catalytic function.

Chenghan Yang, Peng Zhou, Dong-Sheng Zhang et al.

Traditional marine biological image recognition faces challenges of incomplete datasets and unsatisfactory model accuracy, particularly for few-shot conditions of rare species where data scarcity significantly hampers the performance. To address these issues, this study proposes an intelligent marine fish recognition framework, FishAI 2.0, integrating multimodal few-shot deep learning techniques with image generation for data augmentation. First, a hierarchical marine fish benchmark dataset, which provides a comprehensive data foundation for subsequent model training, is utilized to train the FishAI 2.0 model. To address the data scarcity of rare classes, the large language model DeepSeek was employed to generate high-quality textual descriptions, which are input into Stable Diffusion 2 for image augmentation through a hierarchical diffusion strategy that extracts latent encoding to construct a multimodal feature space. The enhanced visual-textual datasets were then fed into a Contrastive Language-Image Pre-Training (CLIP) based model, enabling robust few-shot image recognition. Experimental results demonstrate that FishAI 2.0 achieves a Top-1 accuracy of 91.67 percent and Top-5 accuracy of 97.97 percent at the family level, outperforming baseline CLIP and ViT models with a substantial margin for the minority classes with fewer than 10 training samples. To better apply FishAI 2.0 to real-world scenarios, at the genus and species level, FishAI 2.0 respectively achieves a Top-1 accuracy of 87.58 percent and 85.42 percent, demonstrating practical utility. In summary, FishAI 2.0 improves the efficiency and accuracy of marine fish identification and provides a scalable technical solution for marine ecological monitoring and conservation, highlighting its scientific value and practical applicability.

Xiaoyong Pan, Junchi Yan

RNA-binding proteins (RBPs) play crucial roles in many biological processes, e.g. gene regulation. Computational identification of RBP binding sites on RNAs are urgently needed. In particular, RBPs bind to RNAs by recognizing sequence motifs. Thus, fast locating those motifs on RNA sequences is crucial and time-efficient for determining whether the RNAs interact with the RBPs or not. In this study, we present an attention based convolutional neural network, iDeepA, to predict RNA-protein binding sites from raw RNA sequences. We first encode RNA sequences into one-hot encoding. Next, we design a deep learning model with a convolutional neural network (CNN) and an attention mechanism, which automatically search for important positions, e.g. binding motifs, to learn discriminant high-level features for predicting RBP binding sites. We evaluate iDeepA on publicly gold-standard RBP binding sites derived from CLIP-seq data. The results demonstrate iDeepA achieves comparable performance with other state-of-the-art methods.