As ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation, their secondary structures have been the focus of many recent studies. Despite the computing power of supercomputers, computationally predicting secondary structures with thermodynamic methods is still not feasible when the RNA molecules have long nucleotide sequences and include complex motifs such as pseudoknots. This paper presents RNAVLab (RNA Virtual Laboratory), a virtual laboratory for studying RNA secondary structures including pseudoknots that allows scientists to address this challenge. Two important case studies show the versatility and functionalities of RNAVLab. The first study quantifies its capability to rebuild longer secondary structures from motifs found in systematically sampled nucleotide segments. The extensive sampling and predictions are made feasible in a short turnaround time because of the grid technology used. The second study shows how RNAVLab allows scientists to study the viral RNA genome replication mechanisms used by members of the virus family Nodaviridae.

中文翻译：

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RNAVLab：基于网格计算技术研究RNA二级结构的虚拟实验室。

由于核糖核酸 (RNA) 分子在包括基因表达和调控在内的许多生物过程中发挥着重要作用，因此它们的二级结构已成为许多近期研究的焦点。尽管具有超级计算机的计算能力，但当 RNA 分子具有长核苷酸序列并包括假结等复杂基序时，用热力学方法计算预测二级结构仍然不可行。本文介绍了 RNAVLab（RNA 虚拟实验室），这是一个用于研究包括假结在内的 RNA 二级结构的虚拟实验室，使科学家能够应对这一挑战。两个重要的案例研究展示了 RNAVLab 的多功能性和功能。第一项研究量化了它从系统采样的核苷酸片段中发现的基序重建更长二级结构的能力。由于使用了网格技术，广泛的采样和预测在很短的周转时间内变得可行。第二项研究展示了 RNAVLab 如何让科学家们研究诺达病毒科病毒家族成员使用的病毒 RNA 基因组复制机制。