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arXiv 2403.08797cs.NEcs.AI
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模拟分子进化的进化算法:一个新领域提案

Evolutionary Algorithms Simulating Molecular Evolution: A New Field Proposal

Samuel Ginn College of Engineering, Auburn University(奥本大学塞缪尔·吉恩工程学院);College of Agriculture, Auburn University(奥本大学农学院)

James S. L. Browning, Daniel R. Tauritz, John Beckmann

AI总结:

本文提出融合进化算法、机器学习与生物信息学的 EASME 新子领域,以搜索并设计自然界已灭绝或从未出现的全新功能蛋白质。

摘要:

生命基本功能的遗传蓝图编码在 DNA 中,DNA 被翻译成蛋白质——驱动我们大多数代谢过程的引擎。近期基因组测序的进展揭示了极其多样的蛋白质家族,但与所有可能氨基酸序列构成的庞大搜索空间相比,已知功能性家族的集合仍然极小。可以说,自然界拥有的蛋白质“词汇量”是有限的。因此,计算生物学家面临的主要问题是:这一词汇量能否扩展,以纳入很久以前灭绝、或者可能从未进化出来的有用蛋白质。我们概述了解决该问题的一种计算方法。通过融合进化算法、机器学习(ML)和生物信息学,我们可以促进开发前所未有的全新蛋白质。我们设想这项工作将形成计算进化的一个新子领域,并将其命名为模拟分子进化的进化算法(EASME)。

英文摘要:

The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity of protein families, but compared to the massive search space of all possible amino acid sequences, the set of known functional families is minimal. One could say nature has a limited protein "vocabulary." The major question for computational biologists, therefore, is whether this vocabulary can be expanded to include useful proteins that went extinct long ago, or maybe never evolved in the first place. We outline a computational approach to solving this problem. By merging evolutionary algorithms, machine learning (ML), and bioinformatics, we can facilitate the development of completely novel proteins which have never existed before. We envision this work forming a new sub-field of computational evolution we dub evolutionary algorithms simulating molecular evolution (EASME).

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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