VfoldCPX: Predicting 2D structures of RNA/RNA complexes


To avoid long computational time, we restrict the total sequence length (RNA1 + RNA2) based on the coverage of the conformational ensemble:
(1) ≤300 nt for the ensemble of RNA secondary (without crossing base pairs) structures.
(2) ≤150 nt for the ensemble of RNA secondary and H-type pseudoknotted structures.
(3) ≤120 nt for the ensemble of RNA secondary, pseudoknotted, and hairpin-hairpin kissed structures

The thermodynamic parameters for loops/junctions are from the Vfold model and the parameters for base stacks, including mismatched base stacks, are from the Turner parameters (04 version) OR the MFOLD (2.3 version).


(1) Temperature °C

(2) Energy paramters for base stacks, including mismatched base stacks:

from the Turner parameters (04 version)

from the MFOLD (2.3 version)

(3) Enter sequences (A,a,U,u,G,g,C,c):

RNA1:

RNA2:

(4) Job name (alphanumeric characters only):

(5) Your email address (optional, you will receive the results by email, if provided):


References for VfoldCPX:
[1] Xu, XJ., Zhao, PN., Chen, SJ. (2014) Vfold: a web server for RNA structure and folding thermodynamics prediction. PLoS ONE doi: 10.1371/journal.pone.0107504.
[2] Cao, S, Xu, XJ., Chen, SJ. (2014) Predicting Structure and Stability for RNA Complexes with Intermolecular Loop-loop Base Pairing. RNA, 20:835-45. doi: 10.1261/rna.043976.113
[3] Cao, S. and Chen, S.-J. (2012) Predicting kissing interactions in microRNA-target complex and assessment of microRNA activity. Nucleic Acids Res. 40(10):4681-4690;
[4] Cao, S. and Chen, S.-J. (2011) Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal. RNA. 17: 2130-2143;
[5] Cao, S. and Chen, S.-J. (2006) Free energy landscapes of RNA/RNA complexes - with applications to snRNA complexes in spliceosomes. Journal of Molecular Biology 356: 292-312;

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