它的算法和理论支持主要来源于M. Zuker和P. Stiegler在1981年发表的这篇Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information.想了解Michael Zuker教授小组的一系列研究情况和MFE算法计算依据的可以点这里。 Vienna RNA Package的下载地址是http://www.tbi.univie.ac.at/~ivo...
参考资料 Kagaya, Y., Zhang, Z., Ibtehaz, N., Wang, X., Nakamura, T., Punuru, P. D., & Kihara, D. (2025). NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation. Nature communications, 16(1), 881....
p pBackground/p pThe prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a set of aligned sequences, is one of the oldest and most widely ...
在计算领域中，近期一些基于深度学习的方法将RNA序列作为输入，并使用循环神经网络RNN，例如 LSTM 和GRU等模型对不同碱基之间的相互作用进行建模，进而实现二阶结构预测。但是，RNN 模型需要按顺序运行，这会导致训练和推理存在局限性。 作者模型的输入由序列中所有可能的碱基对的图结构组成，而不是使用核苷酸序列本身。...
p pBackground/p pThe prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a set of aligned sequences, is one of the oldest and most widely ...
54, 81 Furthermore, RNAP pausing has been shown to influence RNA folding pathways, either by giving time for the RNA to rearrange into more thermodynamically stable structures or by selecting for certain metastable structures that prevent downstream sequence from interfering with labile folds.63 ...
p : / / n a r . o x f o r d j o u r n a l s . o r g / D o w n l o a d e d f r o m (3) Figure of input page with verbose input expanded. (4) Definitions of all structural measures. WEB SERVER RNAiFold is a web server that provides access to two too...
RNAfold -p < input.fa ``` - 输出中包括热力学集群的自由能、MFE结构在集群中的频率和集群多样性。例如: ``` frequency of mfe structure in ensemble 0.20997; ensemble diversity 4.19 ``` 3. **最大期望准确性(MEA)结构**: - 通过 `-MEA` 选项可以计算最大期望准确性结构,这是对预测准确性的度量...
T.P. Calmels, I. Callebaut, I. Leger, P. Durand, A. Bril, J.P. Mornon, M. Souchet Sequence and 3D structural relationships between mammalian Ras- and Rho-specific GTPase-activating proteins (GAPs): the cradle fold FEBS Lett, 426 (1998), pp. 205-211 View PDFView articleView in Sc...
RNAfold[-p[0|2]] [-C] [-Ttemp] [-4] [-d[0|1|2|3]] [-noLP] [-noGU] [-noCloseGU] [-e1|2] [-Pparamfile] [-nsppairs] [-Sscale] [-circ] [-MEA [gamma]] DESCRIPTION RNAfoldreads RNA sequences from stdin, calculates their minimum free energy (mfe) structure and prints...