Server for Structural Biology

vsfold4 and 5, vs_subopt: A new paradigm for finding optimal RNA secondary structures and pseudoknots by thermodynamics alone

vsfold4 server (secondary structure only)

vsfold5 server (secondary structure and pseudoknots)

vs_subopt server (secondary structure and pseudoknots)


  1. Dawson, W., Suzuki, K. and Yamamoto, K. (2001) A physical origin for functional domain structure in nucleic acids as evidenced by cross-linking entropy. J Theor Biol. 213, 359-386 and 387-412.
  2. Dawson, W., Kawai, G., and Yamamoto, K. (2005) Modeling the long range entropy of biopolymers: A focus on protein structure prediction and folding. Recent Res. Devel. Experimental & Theoretical Biol., 1, 57-92. isbn: 81-7895-167-3
  3. Dawson, W., Fujiwara, K., Futamura, Y., Yamamoto, K., and Kawai, G. (2006) A method for finding optimal RNA secondary structures using a new entropy model (vsfold). Nucleosides, Nucleotides, and Nucleic Acids 25, 171-189.
  4. Dawson, W., Fujiwara, K., and Kawai, G. (2007). Prediction of RNA pseudoknots using heuristic modeling with mapping and sequential folding. PLoS One, 2, 905.
  5. Dawson, W., Takai, T., Ito, N., Shimizu, K. and Kawai, G. (2014) A new entropy model for RNA: part III. Is the folding free energy landscape of RNA funnel shaped?, Journal of Nucleic Acids Investigation 5 2652.

vswindow and GenoPoemics : A visualization system of RNA secondary structures for longer RNA.

vswindow and GenoPoemics (visualization of secondary structure)


  1. Nakamura, S. (2009) A Novel Virtual Spectrometry: Visualized Regulatory Motifs on ADM, rPolΒ and CD83 mRNAs in Human-friendly Manners, J. Biochem. 146, 251-261 (doi:10.1093/jb/mvp064)

CSNA: Classification System for Nucleic Acid structure determination

CSNA is a computational system to classify RNA structures by its structural character. In the first step, CSNA lists up all the hydrogen bonds and base-base stackings in the structures and classify structures to sub-groups based on their pattern. In the second step, the sub-groups are further classified to groups based on the frequency score (*) and difference between the patterns.

* Frequency score was defined as the sum of the frequency of existing hydrogen bonds or base-base stackings for each sub-group. According to the frequency score, CSNA suggests the most feasible group.

CSNA version 1.0

Please prepare a gzip-compressed tar archive (*.tar.gz) of your structures.
Filename for each structure must be sequentially numbered as file_001.pdb, file_002.pdb... (or file1.pdb, file2.pdb... etc.).


  1. Takasu, A., Kawai, G., Watanabe, K. (1999) Development of a system to classify 3D structural character of RNA, Nucleic Acids Symp. Ser. 42, 233-234.
  2. Takasu, A., Kawai, G., Watanabe, K. (2000) Classification of 3D structural character of RNA by hydrogen bond and base stacking. Nucleic Acids Symp. Ser. 44, 227-228.
  3. Takasu, A., Watanabe, K. and Kawai, G. (2002) Classification of RNA Structures Based on Hydrogen Bond and Base-Base Stacking Patterns: Application for NMR structures, J. Biochem. 132, 211-215.
  4. Baba, S., Takasu, A., Watanabe, K. and Kawai, G. (2003) Application of the RNA structure classification system, CSNA, to NMR structure determination, Nucleic Acids Res. Supplement 3, 127-128.
  5. Someya, T., Sakamoto, T., Takasu, A. and Kawai, G. (2004) Analysis of local convergence in NMR structure calculation for RNA by a classification system for nucleic acid structure, CSNA. Nucleosides, Nucleotides & Nucleic Acids, 23, 691-700.

RELP: Database of Relative Positions of Ribonucleotide Bases in a Crystal Structure of Ribosome

Sorry. Now under preparation.


  1. Takasu, A., Watanabe, K. and Kawai, G. (2002) Analysis of Relative Positions of Ribonucleotide Bases in a Crystal Structure of Ribosome, Nucleosides, Nucleotides and Nucleic Acids@21 449-462

Questions and commnets

last modified: May 27, 2015