Vfold Pipeline offers a new user-friendly approach to the fully automated prediction of RNA 3D structures with given sequences. It first predicts 2D structures using the Vfold2D model [1-6] and then predicts 3D structures based on the predicted 2D structures using the Vfold3D [7] and VfoldLA [8] models. The Vfold3D/VfoldLA methods are based on the assembly of A-form helices with loop and/or motif templates, extracted from the known RNA 3D structures.
Due to the limitation of the current template library, Vfold Pipeline may give no predictions.

The standalone version of the Vfold-Pipeline package can be downloaded via the following link.
VfoldPipeline_standalone.tar.bz2 (1.6 GB)
The details about the Vfold-Pipeline server and standalone package can be found below:

Submit a new job:
In Example 1, the server first predicts 2D structures without H-type pseudoknot and then predicts 3D structures for tRNA 1ffy.
The final output page for example 1.

   Download example SHAPE file      View example SHAPE file in a new tab
In example 2, the server first predicts 2D structures including H-type pseudoknot given SHAPE restraints and then predicts 3D structures for RNA 1e95. Users should download the above example SHAPE file and then upload it using the upload button in item (6). Users can also just view the content of the example SHAPE file via the link above.
The final output page for example 2.

In example 3, the server predicts 3D structures for RNA 1e95 with the user given 2D structure.
The final output page for example 3.

(1) Enter sequence (only single stranded; ≤300 nucleotides; only accept AUGCaugc):

(2) 2D structure in dot-bracket format (optional; only accept .()[]<>{}; If not given, 2D structure will be predicted by program Vfold2D):

(3) Maximum number of predicted 2D structures to be used for predicting 3D structures:

(4) Consider H-type pseudoknot when predicting 2D structure: No Yes

(5) Temperature used for predicting 2D structure: °C

(6) SHAPE file used for predicting 2D structures (optional): SHAPE file format

(7) Excluded templates (labeled by PDB ids) from database when generating 3D structures by Vfold3D/VfoldLA (optional):

(8) Job name (≤10 alphanumeric characters):

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

(10) Anti-robot:

References for Vfold Pipeline:
[1] Xu, XJ., Chen, S.-J. (2016) A method to predict the structure and stability of RNA/RNA complexes. Methods Mol Biol. 1490:63-72.
[2] Xu, XJ., Chen, S.-J. (2015) Modeling the structure of RNA scaffold. Methods Mol Biol. 1316: 1-11.
[3] Xu, XJ., Zhao, PN., Chen, S.-J. (2014) Vfold: a web server for RNA structure and folding thermodynamics prediction. PLoS ONE
[4] Cao, S., Chen, S.-J. (2009) Predicting structures and stabilities for H-type pseudoknots with inter-helix loop. RNA, 15, 696-706.
[5] Cao, S., Chen, S.-J. (2006) Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Research, 34, 2634-2652.
[6] Cao, S., Chen, S.-J. (2005) Predicting RNA folding thermodynamics with a reduced chain representation model. RNA, 11, 1884-1897.
[7] Cao, S., Chen, S.-J. (2011) Physics-based de novo prediction of RNA 3D structures. The Journal of Physical Chemistry B, 115:4216-4226.
[8] Xu, XJ., Chen, S.-J. (2017) RNA three-dimensional structure prediction using hierarchical loop template assembly.
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