PhaSepDB 3.0: a comprehensive knowledgebase of phase separation-related proteins from AI-assisted curation.

IF 13.1 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2025-10-08 DOI:10.1093/nar/gkaf973

Kaiqiang You,Runyu Li,Ruixin Lian,Yuxuan Li,Hongzhining Yang,Yiran Zhou,Yangsheng Chen,Likun Wang,Zhaoqing Fan,Liwei Ma,Tingting Li

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引用次数: 0

Abstract

Phase separation (PS) is a fundamental principle driving the formation of membraneless organelles (MLOs), which are critical for various cellular functions and pathological conditions. We present PhaSepDB 3.0 (https://db.phasep.pro/), a significantly updated knowledgebase of proteins related to PS. To address the challenges of curating a vast body of literature, we have implemented a novel human-AI collaborative workflow that integrates a large language model (LLM)-based agentic system with expert verification, enabling a major expansion and enrichment of the database. PhaSepDB 3.0 now contains 3,484 expert-curated entries for 1849 PS-related proteins, more than doubling the content of the previous version. The annotation framework has been restructured to capture deeper insights, including functional relevance, experimental evidence, and the intrinsic and extrinsic regulations of PS. A key new feature is the protein-wise summary page, which synthesizes data from multiple publications to provide a comprehensive overview of each protein's PS behaviour and functional relevance. With redesigned, user-friendly web interfaces, PhaSepDB 3.0 serves as a critical resource for the community, supporting researchers to explore the intricate basis of PS and its biological implications in greater detail.

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PhaSepDB 3.0：人工智能辅助培养的相分离相关蛋白质的综合知识库。

相分离（PS）是驱动无膜细胞器（MLOs）形成的基本原理，它对各种细胞功能和病理状态至关重要。我们提出了PhaSepDB 3.0 （https://db.phasep）。pro/)，一个与PS相关的蛋白质的重要更新知识库。为了解决管理大量文献的挑战，我们实施了一种新的人类-人工智能协作工作流，该工作流集成了基于大型语言模型（LLM）的代理系统和专家验证，从而实现了数据库的重大扩展和丰富。PhaSepDB 3.0现在包含3,484个专家策划的1849个ps相关蛋白质条目，比以前版本的内容增加了一倍多。对注释框架进行了重组，以获得更深入的见解，包括功能相关性、实验证据以及PS的内在和外在调节。一个关键的新功能是蛋白质方面的摘要页面，该页面综合了来自多个出版物的数据，以提供每种蛋白质的PS行为和功能相关性的全面概述。通过重新设计，用户友好的web界面，PhaSepDB 3.0作为社区的重要资源，支持研究人员更详细地探索PS的复杂基础及其生物学含义。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.