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Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

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Updated: May 7, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

使用尺度不变特征转换算法来对齐距离矩阵有助于系统的蛋白质结构比较.

Zhengyang Guo¹, Yang Wang¹, Guangshuo Ou¹

¹Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, McGovern Institute for Brain Research, State Key Laboratory of Membrane Biology, School of Life Sciences and MOE Key Laboratory for Protein Science, Tsinghua University, Beijing 100084, China.

Bioinformatics (Oxford, England)

|February 6, 2024

概括

调整距离矩阵与尺度 (ADAMS) 管道提供了高效的蛋白质结构比较. 亚当斯准确地识别了相似之处,即使是灵活的蛋白质,匹配Foldseek.

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科学领域:

结构生物信息学结构生物信息学
计算生物学是一种计算生物学.
蛋白质科学是一种蛋白质科学.

背景情况:

蛋白质结构的比较对于理解蛋白质的功能,同质性和进化至关重要.
在in-silico蛋白质结构预测方面的进步产生了大量的模型,需要有效的比较工具.
现有的方法面临挑战,因为蛋白质具有显著的结构灵活性,特别是当序列相似性较低时.

研究的目的:

开发一个新的管道,ADAMS (调整距离矩阵与尺度),用于大规模的蛋白质结构比较.
解决结构灵活蛋白质比较方面的局限性.
提供一种性能和准确度与Foldseek.com等现有方法相比较的工具.

主要方法:

开发了ADAMS管道,将距离矩阵对齐与规模不变特征转换算法集成在一起.
采用计算机视觉为中心的方法来比较距离矩阵.
评估了ADAMS与现有的工具对性能,准确性和灵活蛋白质结构的处理进行了评估.

主要成果:

亚当斯展示了与Foldseek.seek相当的性能和精度.
ADAMS有效地处理具有高结构灵活性的蛋白质,克服了其他工具的局限性.
该管道提供了一种简化的方法来进行蛋白质基尺度蛋白质结构比较.

结论:

亚当斯是深入分析蛋白质结构的有效工具,提供更高的准确性.
该管道为比较蛋白质结构,特别是具有灵活性的蛋白质结构提供了一个有价值的替代方案.
作为一个Python包,ADAMS可以访问,源代码和在线服务器可用.