Review ArticlesNo Access

SOLVING ION CHANNEL KINETICS WITH THE QuB SOFTWARE

CHRISTOPHER NICOLAI

Physiology and Biophysics, SUNY Buffalo, 301 Cary Hall, Buffalo, NY 14214, USA

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and

FREDERICK SACHS

Physiology and Biophysics, SUNY Buffalo, 301 Cary Hall, Buffalo, NY 14214, USA

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https://doi.org/10.1142/S1793048013300053Cited by:110 (Source: Crossref)

Abstract

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.

Special Issue Comment: This is a review about the software QuB that can extract a model from the trajectory. It is connected with the review about treatments when solving single molecules,⁶⁰ and the reviews about enzymes.^61,62

Keywords:

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