BioPipelines: Accessible Computational Protein and Ligand Design for Chemical Biologists [0.03%]
生物流水线：化学生物学家常用的计算蛋白质和配体设计的便捷工具
Gianluca Quargnali,Pablo Rivera-Fuentes
Gianluca Quargnali
Deep learning methods for protein structure generation, sequence design, and structure and property prediction have created unprecedented opportunities for protein engineering and drug discovery. However, using these tools often requires na...
Integrated Multi-Tissue Transcriptomics Reveals Antagonistic Pleiotropy in Aging and Alzheimer's Disease [0.03%]
整合多组织转录组学揭示了衰老与阿尔茨海默病的拮抗多效性
Rana Salihoglu,Şehnaz Can,Thomas Dandekar et al.
Rana Salihoglu et al.
Aging is the strongest risk factor for Alzheimer's disease (AD); however, some individuals age without major cognitive decline, suggesting that resilience and vulnerability may be associated with distinct molecular trajectories. To investig...
Family-Specialized Transformer for L-cystathionine gamma-lyase Engineering and Its Structural Interpretation [0.03%]
家庭专用变压器L半胱硫醚伽马裂解酶工程及其结构解释
Ungyu Lee,Minho Park,Byungkun Song et al.
Ungyu Lee et al.
The diversity of protein structures and reaction mechanisms complicates general-purpose artificial intelligence models for enzyme engineering, motivating family-specialized models. In this study, we developed EnzFormer, a specialized artifi...
Graph Topology Reframes the Coherence of Cell-State Manifold Inference under Heterogeneous Single-Cell Observations [0.03%]
图拓扑学重新定义了异质单细胞观测下细胞状态流形推断的一致性问题
Tomohiro Tamura,Yusuke Yamane,Yuji Okano et al.
Tomohiro Tamura et al.
Manifold-based single-cell omics analyses assume that high-dimensional observations can fall into a low-dimensional space encoding biological constraints. In practice, per-cell observation is highly heterogeneous: Shallowly and deeply obser...
LncRCD: A Comprehensive Database for Pan-Cancer Characterization of lncRNAs Related to 12 Regulated Cell Death Types [0.03%]
LncRCD：与12种调节性细胞死亡类型相关的癌症长链非编码RNA的综合数据库
Hongying Zhao,Lin Bai,Shiyi Li et al.
Hongying Zhao et al.
Regulated cell death (RCD) is a fundamental biological process that determines tumor progression and treatment response. Although high-throughput sequencing technologies have revealed a large number of tumor-related long noncoding RNAs (lnc...
A Systematic Evaluation of Protein Phase Separation Predictors across Diverse Protein Landscapes [0.03%]
全面评估蛋白质相分离预测器在不同蛋白质景观中的表现
Kate E Gilroy,John N Barr
Kate E Gilroy
Background: Liquid-liquid phase separation (LLPS) plays a central role in cellular regulation, with its dysregulation linked to numerous diseases. LLPS is also increasingly implicated in various biological contexts, such as virus replicatio...
Phospholipids that Plug the Pores of Cholesteryl Ester Transfer Protein Control Its Triglyceride Transfer [0.03%]
调控胆固醇脂转移蛋白胆固醇酯交换的鞘氨醇磷脂嵌入胆固醇脂转移蛋白孔道的能力
Sukriti Sacher,Praveen Singh,Abhishek Mukherjee et al.
Sukriti Sacher et al.
Cholesteryl ester transfer protein (CETP), a key drug target in cardiovascular disease, primarily regulates plasma circulating levels of lipids (within high, low, and very-low-density lipoproteins). In addition to its terminal openings, CET...
Protein Design Enters the Artificial Intelligence Era: Foundations, Tools, and Emerging Paradigms [0.03%]
蛋白质设计进入人工智能时代：基础、工具和新兴范式
Yanlin Mi,Arpit Shukla,Mark Tangney et al.
Yanlin Mi et al.
Artificial intelligence (AI) has transformed protein engineering by leveraging deep learning, protein language models, and knowledge graphs to decode relationships between sequence, structure, and function. Models like AlphaFold2 achieve ne...
Integrative Multiomics and Single-Cell Profiling Identify TNFRSF1A+ Macrophages as a Prognostic and Therapeutic Target in Diffuse Large B-cell Lymphoma [0.03%]
整合多组学和单细胞分析鉴定TNFRSF1A+巨噬细胞作为弥漫性大B细胞淋巴瘤中的预后和治疗靶点
Wenxian Yin,Xingyue Wang,Zhuo Chen et al.
Wenxian Yin et al.
The tumor microenvironment plays a critical role in therapeutic resistance in diffuse large B-cell lymphoma (DLBCL), yet actionable targets within the immune cells remain largely undefined. Through integrative multiomics profiling, we ident...
Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations [0.03%]
基于分子动力学模拟接触持续性分析的稳定性驱动配体构象预测及配体设计
Mochammad Arfin Fardiansyah Nasution,Gert-Jan Bekker,Suyong Re et al.
Mochammad Arfin Fardiansyah Nasution et al.
Molecular dynamics simulations provide deep insights into protein-ligand interactions, but their high computational cost often limits their application in early-stage drug design. To address this issue, we developed a computational workflow...