NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

The Nearest Neighbor Database (NNDB, http://rna.urmc.rochester.edu/NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters, the database includes the set of rules with descriptive text, sequence-dependent parameters in plain text and html, literature references to experiments and usage tutorials. The initial release covers parameters for predicting RNA folding free energy and enthalpy changes.

[1]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[2]  Kevin P. Murphy,et al.  Efficient parameter estimation for RNA secondary structure prediction , 2007, ISMB/ECCB.

[3]  Shi-Jie Chen,et al.  Predicting structures and stabilities for H-type pseudoknots with interhelix loops. , 2009, RNA.

[4]  J. SantaLucia,et al.  The thermodynamics of DNA structural motifs. , 2004, Annual review of biophysics and biomolecular structure.

[5]  Jan Barciszewski,et al.  RNA Biochemistry and Biotechnology , 1999 .

[6]  D. Turner,et al.  Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. , 1998, Biochemistry.

[7]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[8]  D. Turner,et al.  A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation , 2006, Nucleic acids research.

[9]  D. Turner,et al.  Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[10]  J. SantaLucia,et al.  A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[11]  R. Knight,et al.  From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal. , 2008, RNA.

[12]  D. Crothers,et al.  Improved estimation of secondary structure in ribonucleic acids. , 1973, Nature: New biology.

[13]  Anne Condon,et al.  RNAsoft: a suite of RNA secondary structure prediction and design software tools , 2003, Nucleic Acids Res..

[14]  C. Pleij,et al.  An approximation of loop free energy values of RNA H-pseudoknots. , 1999, RNA.

[15]  Song Cao,et al.  Predicting RNA pseudoknot folding thermodynamics , 2006, Nucleic acids research.

[16]  Ye Ding,et al.  Sfold web server for statistical folding and rational design of nucleic acids , 2004, Nucleic Acids Res..

[17]  Michael Zuker,et al.  Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide , 1999 .

[18]  Serafim Batzoglou,et al.  CONTRAfold: RNA secondary structure prediction without physics-based models , 2006, ISMB.

[19]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[20]  Niles A. Pierce,et al.  A partition function algorithm for nucleic acid secondary structure including pseudoknots , 2003, J. Comput. Chem..