SOLVING ION CHANNEL KINETICS WITH THE QuB SOFTWARE
SOLVING ION CHANNEL KINETICS WITH THE QuB SOFTWARE
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DOI：
10.1142/s1793048013300053
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发表时间：
2013-12-01
期刊：
影响因子：
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通讯作者：
Sachs, Frederick
中科院分区：
文献类型：
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作者：
Nicolai, Christopher;Sachs, Frederick
记录单个离子通道电流的能力导致需要从这些数据中提取潜在的动力学模型。这种逆隐马尔可夫问题很困难，但导致了利用似然优化的名为 QuB 的软件套件的创建。这篇评论介绍了该软件。该软件是开源的，除了求解动力学模型外，还具有许多通用数据库操作，包括生成带有可发布图形的报告、函数拟合和用于新的和重复处理的脚本以及 AD/DA I/O。核心算法允许固定利率或维持模型中的详细平衡等约束。所有速率常数都可以由刺激驱动，并且系统可以分析非平稳数据。 QuB 还可以分析无法区分单个事件的多通道数据的动力学，但拟合算法利用信号方差以及均值来拟合模型。 QuB 可以应用于任何用马尔可夫动力学适当建模的数据，并已用于解决离子通道问题，还可以解决运动蛋白的运动、小鼠睡眠周期和物理过程的问题。
The ability to record the currents from single ion channels led to the need to extract the underlying kinetic model from such data. This inverse hidden Markov problem is difficult but led to the creation of a software suite called QuB utilizing likelihood optimization. This review presents the software. The software is open source and, in addition to solving kinetic models, has many generic database operations including report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. The core algorithms allow for constraints such as fixed rates or maintaining detailed balance in the model. All rate constants can be driven by a stimulus and the system can analyze nonstationary data. QuB also can analyze the kinetics of multichannel data where individual events cannot be discriminated, but the fitting algorithms utilize the signal variance as well as the mean to fit models. QuB can be applied to any data appropriately modeled with Markov kinetics and has been utilized to solve ion channels but also the movement of motor proteins, the sleep cycles in mice, and physics processes.