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DNAlive extends, for the first time, genomic analysis to the three-dimensional exploration of DNA-protein systems. The programme uses pre-computed equilibrium values for helical parameters (twist, roll, tilt, rise, shift and slide) of the 10 unique base steps (d(GG), d(GA), d(GT), d(GC), d(AA), d(AG), d(AT), d(CG), d(CA) and d(TA)). Equilibrium parameters implemented here were obtained from extensive molecular dynamics simulations performed in water with the new parmbsc0 force-field.
Protein-DNA complexes are visualized by substituting the naked coordinates of the fiber with PDB data in the segment in which this is available. When the Jmol applet has loaded onto your web browser, you can activate any Jmol feature (such as edit, centre, zoom, ...) or use our integrated buttons to navigate through the structure. Using JMOL you can analyse the structure in many ways, including distance measures, van der Waals contacts,... Just press the right button on your mouse.
If you select specific physical properties to be visualize (previous screen), you must click on "Paint the..." button.
Here you will find more information on the interpretation of the results
As you can see in this image, a colour code is used to display the value of the property.
The red areas indicate that the value of the property in that nucleotide is high, while blue areas indicate that the value is low.
White is used for nucleotides whose value is unknown, like those at the ends of the DNA. Proteins are depicted in green.