Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.
J Biomol Struct Dyn. 2011 Apr;28(5):815-26. doi: 10.1080/07391102.2011.10508609.
Computational prediction of RNA tertiary structures is a significant challenge, especially for longer RNA and pseudoknots. At present it is still difficult to do this by pure all-atom molecular dynamics simulation. One of possible approaches is through hierarchical steps: from sequence to secondary structure and then to tertiary structure. Here we present improvements of two key steps of this approach, the manual adjustment of atom clashes and bond stretches and molecular dynamics refinement. We provide an energy function to find the locations of atom clashes and bond stretches and to guide their manual adjustment and a new scheme of molecular dynamics refinement using a tested combination of solvent model and the ff98 Amber force field suitable for RNA. We predicted with higher accuracy the tertiary structures of nine typical RNA molecules of lengths from 12 to 52, including hairpins, duplex helices and pseudoknots.
计算 RNA 三级结构的预测是一项重大挑战，尤其是对于较长的 RNA 和假结。目前，通过纯全原子分子动力学模拟仍然难以做到这一点。一种可能的方法是通过分层步骤：从序列到二级结构，然后到三级结构。在这里，我们介绍了该方法的两个关键步骤的改进，即原子碰撞和键拉伸的手动调整以及分子动力学精修。我们提供了一种能量函数来找到原子碰撞和键拉伸的位置，并指导它们的手动调整，以及一种使用经过测试的溶剂模型和适合 RNA 的 ff98 Amber 力场的新分子动力学精修方案。我们以更高的精度预测了 9 个典型 RNA 分子的三级结构，这些 RNA 分子的长度从 12 到 52 个核苷酸不等，包括发夹、双链螺旋和假结。
