The web service DNATCO (dnatco.org) classifies local conformations of DNA molecules beyond their traditional sorting to A, B and Z DNA forms. DNATCO provides an interface to robust algorithms assigning conformation classes called NTC: to dinucleotides extracted from DNA-containing structures uploaded in PDB format version 3.1 or above. The assigned dinucleotide NTC: classes are further grouped into DNA structural alphabet NTA: , to the best of our knowledge the first DNA structural alphabet. The results are presented at two levels: in the form of user friendly visualization and analysis of the assignment, and in the form of a downloadable, more detailed table for further analysis offline. The website is free and open to all users and there is no login requirement.

Institute of Biotechnology CAS BIOCEV Průmyslová 595 252 50 Vestec Prague West Czech Republic

See more in PubMed

Berman H.M., Westbrook J., Feng Z., Iype L., Schneider B., Zardecki C. The nucleic acid database. Acta Crystallogr. D Biol. Crystallogr. 2002;58:889–898. PubMed

Lu X.J., Olson W.K. 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat. Protoc. 2008;3:1213–1227. PubMed PMC

Svozil D., Kalina J., Omelka M., Schneider B. DNA conformations and their sequence preferences. Nucleic Acids Res. 2008;36:3690–3706. PubMed PMC

Cech P., Kukal J., Cerny J., Schneider B., Svozil D. Automatic workflow for the classification of local DNA conformations. BMC Bioinformatics. 2013;14:205. PubMed PMC

Humphrey W., Dalke A., Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 1996;14:27–38. PubMed

Hanson R.M., Prilusky J., Renjian Z., Nakane T., Sussman J.L. JSmol and the next-generation web-based representation of 3D molecular structure as applied to proteopedia. Isr. J. Chem. 2013;53:207–216.

Drew H.R., Wing R.M., Takano T., Broka C., Tanaka S., Itakura K., Dickerson R.E. Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl. Acad. Sci. U.S.A. 1981;78:2179–2183. PubMed PMC

Neidle S. Principles of Nucleic Acid Structure. Cambridge: Academic Press, Elsevier; 2008. pp. 1–289.

Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses

Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks

Structural variability of CG-rich DNA 18-mers accommodating double T-T mismatches

Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org

A unified dinucleotide alphabet describing both RNA and DNA structures

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

A DNA structural alphabet provides new insight into DNA flexibility

A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle