Nearest Neighbor Database

Published

September 15, 2023

Welcome

Nearest neighbor parameters for RNA folding are used widely in software packages, but no current published source exists to provide the parameters and a tutorial for their use. This database serves this function for the community and is intended to grow as the parameters are refined. The site will also be used to provide a historical record of parameter sets as they are subsequently refined.

Contents

RNA (Turner 2004)

These are the current set of nearest neighbor parameters for RNA folding compiled by the Turner group. Both free energy changes at 37 ºC and enthalpy changes have been estimated, allowing for structure prediction at arbitrary temperature. Parameters are available for download in text format or html format. A description of the functional form and tutorials for use are available.

Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M. and Turner, D.H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA, 101, 7287-7292.

RNA (Turner 1999)

These are the set of nearest neighbor parameters for RNA folding compiled by the Turner group in 1999. The parameters are for estimating free energy changes at 37 ºC. Parameters are available for download in text format or html format. A description of the functional form and tutorials for use are available.

Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H. (1999) Expanded sequence dependence of thermodynamic parameters provides improved prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.

DNA (RNAstructure)

These are the set of nearest neighbor parameters for DNA folding compiled by the Mathews group and released as part of RNAstructure package. Both free energy changes at 37 ºC and enthalpy changes have been estimated, allowing for structure prediction at arbitrary temperature. Parameters are available for download in text and html format. A description of the functional form and tutorials for use are available.

Reuter, J. S., & Mathews, D. H. (2010). RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics, 11, 129.

RNA + m6A (Kierzek et al.)

These are the set of nearest neighbor parameters for RNA folding with N6-methyladenosine (m6A) modification compiled by Kierzek et al. The parameters are for estimating free energy changes at 37 ºC. Parameters are available for download in text and html format. A description of the functional form and tutorials for use are available.

Kierzek, E., Zhang, X., Watson, R. M., Kierzek, R., Mathews, D. H. (2022). Secondary Structure Prediction for RNA Sequences Including N6-methyladenosine. Nature Communications, 13, 1271.

Reference

Research benefiting from this website should please cite:

Turner, D. H. & Mathews, D. H. (2009). NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Research. 38, D280-D282.

Download

Download NNDB as PDF ebook.

Contact

This page is maintained by the Mathews lab at the University of Rochester. Please contact David Mathews David_Mathews@urmc.rochester.edu with comments or questions.