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NTDB


NAR Molecular Biology Database Collection entry number 273
Chiu, W. L. A. K., Sze, C. N., Ma, N. T., Chiu, L. F., Leung, C. W., Au-Yeung, S. C. F.
Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China

Database Description

The second release of Thermodynamic Database for Nucleic Acids, NTDB 2.0, includes more than 4600 entries (250% increase over release 1.0). It contains sequence types and details of several thermodynamic parameters (enthalpy, DH; entropy, DS; Gibbs free energy, DG; melting temperature, Tm), experimental models and methods for extracting thermodynamic parameters, buffer conditions as well as all relevant literature information. In addition, the database statistics and references related to NTDB are included. Information on normal and modified nucleobases and nucleosides are collected in a new section 'Nucleoside' whereby data collected thus far will be release in NTDB 2.0. The NTDB is available at http://ntdb.chem.cuhk.edu.hk freely.

Recent Developments

In this release, the number of entries of NTDB has been increased to 4640, which is about a 2.5 times increase in the number of entries reported compared to the first release. Thermodynamics data determined by circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMR) are included and these categories are added as search items under 'experimental method'. Moreover, both methods and models (e.g. the two-state model) are included for extraction of thermodynamic parameters from experiments. Furthermore, a new 'Nucleoside' section, which shows the structure, its IUPAC and common names, the NTDB notation, the molecular formula as well as links retrieving chemical and physical properties (NIST Webbook) and cancer screening data (Developmental Therapeutics Program, DCTD, National Cancer Institute), is added where all relevant information associated with normal and modified nucleobases and nucleosides are collected. The database statistics and the references related to NTDB are included in NTDB.

Acknowledgements

This work is partially supported by two The Chinese University of Hong Kong (CUHK) Direct Grants (Grant nos.: 2060156 and 2060179) and the Goldlion Fund (Ref. No.: G01125) of Hong Kong SAR. W. L. A. K. Chiu acknowledges the financial support from the Research Grant Council of Hong Kong SAR, Central Allocation Scheme ? and a Faculty of Science Special Grant, CUHK.

References

1. Chiu,W.L.A.K.; Sze,C.N.; Yip,L.N.;supfam Chan,S.K.; Au-Yeung,S.C.F. (2001) NTDB: Thermodynamic Database for Nucleic Acids. Nucleic Acids Res. 29, 230-233.
2. Freier,S.M. and Altmann,K.-H. (1997) The ups and downs of nucleic acid duplex stability: Structure-stability studies on chemically modified DNA:RNA duplexes. Nucleic Acids Res. 25, 4429?443.
3. Bairoch,A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45?8.
4. Westbrook,J.; Feng, .; Jain,S.; Bhat,T.N.; Thanki,N.; Ravichandran,V.; Gilliland,G.L.; Bluhm,W.; Weissig,H.; Greer,D.S.; Bourne,P.E. and Berman,H.M. (2002) The Protein Data Bank: unifying the archive. Nucleic. Acids. Res. 30, 245-248.
5. Berman,H.M.; Olson,W.K.; Beveridge,D.L.; Westbrook,J.; Gelbin,A.; Demeny,T.; Hsieh,S.-H.; Srinivasan,A.R. and Schneider,B. (1992) The Nucleic Acid Database: A Comprehensive Relational Database of Three-Dimensional Structures of Nucleic Acids. Biophys. J. 63, 751-759.
6. Wheeler,D.L.; Church,D.M.; Lasn,A.E.; Leipe,D.D.; Madden,T.L.; Pontius,J.U.; Schuler,G.D.; Schriml,L.M.; Tatusova,T.A.; Wagner,L.; Rapp,B.A. (2002) Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res. 30, 13-16.
7. Linstrom,P.J. and Mallard, W.G. Eds., NIST Chemistry WebBook, NIST Standard Reference Database Number 69, July 2001, National Institute of Standards and Technology, Gaithersburg MD, 20899 (http://webbook.nist.gov).
8. Developmental Therapeutics Program NCI/NIH, National Cancel Institute, (http://dtp.nci.nih.gov).

Subcategory: Nucleic acid structure

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