VfoldPipeline: VFOLDPPLN_1ffy

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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.

Job information

JobID*	Seq2D info	Excluded PDB	SHAPE file	Email	Job status	Duration
VFOLDPPLN_1ffy_ZHFU	seq2D_info	excluded_pdblist			Done	4.0 m

Job progress information

STEP 1: Predicting 2D structures by Vfold2D.
2D structure prediction is done. Get 1 npk 2D structure.
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.
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	5	1ffy_npk1_vfold.pdb	1ffy_npk1_vfold.pdb

npk: non-pseudoknot
pk: pseudoknot

Zip file of results: 1ffy_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/