MotivationMethods for simulating the kinetic folding of RNAs by numerically solving the chemical master equation have been developed since the late 90's, notably the programs Kinfold and Treekin with Barriers that are available in the Vienna RNA package. Our goal is to formulate extensions to the algorithms used, starting from the Gillespie algorithm, that will allow numerical simulations of mid-size (~ 60–150 nt) RNA kinetics in some practical cases where numerous distributions of folding times are desired. These extensions can contribute to analyses and predictions of RNA folding in biologically significant problems.
展开▼
机译：从90年代末以来，已经开发了通过数值求解化学主方程来模拟RNA动力学折叠的方法，尤其是Vienna RNA软件包中提供的Kinfold和Treekin with Barriers程序。我们的目标是从Gillespie算法开始，对所用算法进行扩展，从而在需要折叠时间众多分布的实际情况下，对中等大小（〜60–150 nt）RNA动力学进行数值模拟。这些扩展可以有助于分析和预测生物学重大问题中的RNA折叠。
展开▼
