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.

JobID:


Job information

JobID* Seq2D info Excluded PDB SHAPE file Email Job status Duration
VFOLDPPLN_1e95_JZ5d seq2D_info excluded_pdblist example_shape.txt Done 7.0 m

Job progress information

  • STEP 1: Predicting 2D structures by Vfold2D given SHAPE restraints.
  • STEP 1.1: Predicting non-pseudoknotted (npk) 2D structures.
    •         Get 1 npk 2D structure.
  • STEP 1.2: Predicting pseudoknotted (pk) 2D structures.
    •         Get 1 pk 2D structure.
  • 2D structure prediction is done. Get 1 npk and 1 pk 2D structures.
  • STEP 2: Predicting 3D structures by Vfold3D and VfoldLA based on the predicted 2D structures.
  • STEP 2.1: Predicting 3D structures for npk 2D structure #1.
    •         npk 3D structure prediction is done.
  • STEP 2.2: Predicting 3D structures for pk 2D structure #1.
    •         pk 3D structure prediction is done.
  • 3D structure prediction is all done.
  • Task has been completed.

Results

Result summary
2D DBN 2D Figure[9] 3D Number 3D File 3D Figure[10]
npk1 npk1 10 1e95_npk1_vfold.pdb 1e95_npk1_vfold.pdb
pk1 pk1 1 1e95_pk1_vfold.pdb 1e95_pk1_vfold.pdb

npk: non-pseudoknot
pk: pseudoknot

Zip file of results: 1e95_results.zip

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.
[9] Darty, K., Denise, A., Ponty, Y. (2009) VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974-1975
[10] Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/
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