To avoid long computational time, we restrict the total sequence length, the strand length, and the number of strands based on the coverage of the conformational ensemble:
(1) ≤300 nt for the ensemble of RNA secondary (without crossing base pairs) structures.
(2) ≤180 nt for the ensemble of RNA secondary and H-type pseudoknotted structures of the specific strand order (RNA 1 to RNA N).
(3) ≤150 nt for the ensemble of RNA secondary and H-type pseudoknotted structures of all the strand combinations.
(4) ≤9 strands for the total number of RNAs of the specific strand order (RNA 1 to RNA N).
(5) ≤5 strands for the total number of RNAs of all the strand combinations.

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).

Check existing job

Job ID:


Need help?

VfoldMCPX help page


Submit a new job:
Number of RNA strands (2~9):  
ⓘYou can specify a number between 2 and 9 (inclusive).


(1) Temperature (0~200 °C) °C  
ⓘYou can specify a number between 0 and 200 (inclusive).


(2) Energy parameters for base stacks:  
ⓘBase stacking energy parameters, 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):  
ⓘWe recognize A, a, C, c, G, g, U, u. Mininum length is 3-nt.

RNA1:

RNA2:


(4) Job name:  
ⓘAlphanumeric characters only. Note that this is not job ID.


(5) Your email address (optional):  
ⓘTo receive the results by email, please select the checkbox and enter a valid address.





(6) Pseudoknots:  
ⓘPredict secondary structures without or with pseudoknots


no pseudoknots are allowed to form

H-type pseudoknots are allowed to form


(7) Strand order:  
ⓘStrand orders to be considered in the prediction


specific strand order: from RNA 1 to RNA N

all the strand combinations

References for VfoldMCPX:
[1] Zhang S, Cheng Y, Guo P, Chen SJ. VfoldMCPX: Predicting multistrand RNA complexes. RNA. 2022 Jan 20:rna-079020.
[2] 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.
[3] 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
[4] 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;
[5] 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;
[6] 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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