Assignment of DNA conformers (DNATCO v2)

The server assigns 57 DNA conformers (ntC) based on the values of their 9 backbone torsion angles.

Please, read before you upload coordinates of your DNA:

• DNA steps are identified based on atom names as defined by the PDB format, version 3.1 or above (sugar atoms as O4' not O4*).
• Steps with non-standard or missing atoms that define torsions δ ... δ+1, χ, and χ+1 are not considered in the assignment process.
• Conformers are assigned for modified residues that contain standard names for atoms defining the step torsions between δ and δ+1 and χ and χ+1.

Selection of the DNA structure in PDB format:

1. Browse for a locally stored PDB file and press SUBMIT button to upload (left hand side) OR
2. Enter a 4-characters PDB ID and press SUBMIT button (right hand side)

Analysis of results:

1. Click a row of the table to display the assigned step details; Hovering over a row shows the description.
2. Selected step is shown in ball and sticks representation in the interactive JSmol applet. The behavior of the applet can be changed above to center on the analyzed step or the whole molecule.
   Bellow is a short help explaining the applet controls.
3. Step backbone torsion angles are plotted (black line graph) and compared to the distribution of the manually curated data.
   - Violin plot show distribution of torsion angles for the ntC data.
   - Black bar inside indicates 1^st and 3^rd quartile.
   - Mean value is indicated as white point.
   - "Error bars" show the minimum and maximum values satisfying the assignment algorithm.
   - The thumbnail can be used as a reference for definition of backbone torsion angles.
   - The table bellow summarizes the angular values.
4. Download the results as CSV file containing the complete numerical results.
   - The resulting CSV file contains comma separated step_ID, assigned ntC and ntA, 9 torsion angles of the step (δ to χ1),
   for assigned steps also angular distances from the ntC average values.
   The result version string "_v2C20A10" decodes as DNATCO version 2 with conformers (ntC) version 2.0 and structural alphabet (ntA) version 1.0
   - Browse the reference table of conformers and download definition of the conformers as torsion averages (csv) and their esd values (csv)
   or as their Cartesian oordinates of all 57 conformer classes.