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)

References

  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. http://www.plosone.org/doi/pone.0000905.
  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)

References

  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.).

References

  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.

References

  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