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DNATCO specifications

Information


Unique identifier OMICS_16581
Name DNATCO
Interface Web user interface
Restrictions to use None
Input data A crystal, NMR or computer model structure containing DNA.
Input format PDB
Output data A summary of the assigned ntC and ntA classes, an interactive 3D view of the analyzed DNA structure in the JSmol applet, the results of the dinucleotide step assignment in graphical representation, a table of torsion values for the analyzed step, the assigned ntC and their differences.
Output format CSV, HTML
Programming languages Javascript, PHP, Python
Computer skills Basic
Version 2.2
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Bohdan Schneider

Publications for DNATCO

DNATCO citations

 (3)
library_books

A DNA structural alphabet provides new insight into DNA flexibility

2018
Acta Crystallogr D Struct Biol
PMCID: 5786007
PMID: 29372899
DOI: 10.1107/S2059798318000050

[…] of uncharacterized conformers because of the high deformability of DNA molecules.Both NtC classes and CANA letters are assigned automatically to any PDB-formatted DNA structure at the website https://dnatco.org (Černý et al., 2016). A representation of the CANA letters embodied into the molecular graphics of DNA structures allows straightforward visual inspection of the main structural features of […]

library_books

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

2017
Genes
PMCID: 5664128
PMID: 29057824
DOI: 10.3390/genes8100278

[…] ucleotides with all atoms, which define the nine analyzed torsion angles, thus excluding incompletely refined DNA segments from the analysis. The NtC and CANA classes were assigned at the web server, dnatco.org, which also contains a full description of all 44 NtC classes and their membership to the complete set of the 12 CANA alphabet letters.A brief structural annotation of the CANA letters and […]

library_books

Protein flexibility in the light of structural alphabets

2015
Front Mol Biosci
PMCID: 4445325
PMID: 26075209
DOI: 10.3389/fmolb.2015.00020

[…] is the Protein Blocks. For DNA, a structural alphabet was obtained using a new approach of registering torsion angles of a dinucleotide unit combined with Fourier averaging and clustering (http://www.dnatco.org/, Svozil et al., ; Cech et al., ). These structural alphabets describe biopolymer conformations at greater detail than the 3-state protein secondary structure and basic DNA structural types […]

Citations

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DNATCO institution(s)
Institute of Biotechnology CAS, BIOCEV, Vestec, Prague West, Czech Republic
DNATCO funding source(s)
This work was supported by the Czech National Infrastructure for Biological Data (ELIXIR CZ) (LM2015047), ERDF (BIOCEV CZ.1.05/1.1.00/02.0109), Institutional Research Project of the Institute of Biotechnology (RVO 86652036).

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