特里尔:为民主化,可扩展的蛋白质分析和工程设计编排模块化深度学习工作流程
Zachary A Martinez1, Richard M Murray1, Matt W Thomson1
1Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125.
bioRxiv : the preprint server for biology
|November 21, 2023
概括
TRILL是一个平台,通过深度学习简化了蛋白质设计和发现. 它使科学家能够通过集成先进的AI模型来创建新型蛋白质和分析生物数据,使复杂的方法更容易获得.
科学领域:
- 计算生物学 计算生物学
- 人工智能在生物学中的应用
- 蛋白质工程是指蛋白质工程.
背景情况:
- 由于大量的测序数据,深度学习模型越来越多地用于生物学.
- 对于缺乏机器学习专业知识的研究人员来说,大型复杂的模型带来了挑战.
- 蛋白质语言模型从广泛的序列数据中学习生物模式.
研究的目的:
- 介绍TRILL,一个用于蛋白质设计和发现的平台.
- 为了使科学家能够利用先进的深度学习模型用于生物应用.
- 简化创建复杂的AI驱动蛋白质工程工作流程.
主要方法:
- 特里尔集成了最先进的模型,如ESM-2,DifDock和RFDiffusion.
- 它允许链接模型以创建复杂的分析和设计管道.
- 优化的训练策略 (ZeRO-Offload,分布式数据并行) 便于在各种硬件上使用.
主要成果:
- 特里尔可以实现新型蛋白质生成和3D结构预测.
- 研究人员可以提取高维的蛋白质表示,并执行功能分类.
- 该平台支持复杂的模型编排,合并各种AI功能.
结论:
- TRILL 民主化了对生物研究中强大的深度学习工具的访问.
- 它弥合了复杂的人工智能模型和实际科学应用之间的差距.
- 该平台简化了生物学的先进计算方法的集成和使用.
更多相关视频
07:28JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
3.2K
10:37Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
Published on: November 15, 2017
12.0K
相关概念视频
Protein Complex Assembly
10.6K
Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Many viruses self-assemble into a fully functional unit using the infected host cell to...
10.6K
Protein Dynamics in Living Cells
2.1K
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
2.1K
Synthetic Biology
4.8K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
4.8K
Mechanical Protein Functions
4.9K
Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force.
4.9K
Protein Networks
2.3K
2.3K
Mechanical Protein Function
2.0K
2.0K
