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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >ACES: A co-evolution simulator generates co-varying protein and nucleic acid sequences
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ACES: A co-evolution simulator generates co-varying protein and nucleic acid sequences

机译：ACES：共同求导模拟器产生共同不同的蛋白质和核酸序列

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摘要

Sequence-specific and consequential interactions within or between proteins and/or RNAs can be predicted by identifying co-evolution of residues in these molecules. Different algorithms have been used to detect co-evolution, often using biological data to benchmark a methods ability to discriminate against indirect co-evolution. Such a benchmark is problematic, because not all the interactions and evolutionary constraints underlying real data can be known a priori. Instead, sequences generated in silico to simulate co-evolution would be preferable, and can be obtained using aCES, the software tool presented here. Conservation and co-evolution constraints can be specified for any residue across a number of molecules, allowing the user to capture a complex, realistic set of interactions. Resulting alignments were used to benchmark several co-evolutiondetection tools for their ability to separate signal from background as well as discriminating direct from indirect signals. This approach can aid in refinement of these algorithms. In addition, systematic tuning of these constraints sheds new light on how they drive co-evolution between residues. Better understanding how to detect co-evolution and the residue interactions they predict can lead to a wide range of insights important for synthetic biologists interested in o engineering new, orthogonal interactions between two macromolecules.
机译：通过识别这些分子中残基的协同进化，可以预测蛋白质和/或RNA内部或之间的序列特异性和相应的相互作用。不同的算法被用于检测协同进化，通常使用生物数据来测试方法区分间接协同进化的能力。这样的基准是有问题的，因为并不是所有真实数据背后的交互和进化约束都可以先验地知道。相反，在硅片中生成的模拟协同进化的序列更可取，并且可以使用本文介绍的软件工具aCES获得。可以为多个分子中的任何残基指定守恒和协同进化约束，使用户可以捕获一组复杂、真实的相互作用。由此产生的比对被用于测试几种协同进化检测工具，以确定它们能够将信号从背景中分离出来，以及区分直接信号和间接信号。这种方法有助于改进这些算法。此外，对这些约束条件的系统调整为它们如何推动残基之间的协同进化提供了新的思路。更好地理解如何检测协同进化以及它们预测的残余物相互作用，可以为合成生物学家带来广泛的见解，这对他们感兴趣的是在两个大分子之间构建新的正交相互作用。

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