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For medium sequences, the DNAlive web server also allows a dynamic view of DNA flexibility.
Once a region of interest (for JMOL limitations this analysis is currently limited to a hundred base pairs) is selected in the genomic sequence, the server runs a mesoscopic Metropolis Monte Carlo algorithm, where the geometry of each base pair is defined by 3 local rotations (roll, tilt and twist) and translations (slide, shift and rise) and the conformational energy is estimated from the deformation matrix using an harmonic model (see eq.1), where index "i" stands for one of the M base pair steps and index "j" for the six unique helical parameters (ξ) for each step. The equilibrium values for one helical parameter in a given base pair step type and and the associated deformation constant (Kij) were previously determined from molecular dynamics simulations. To optimize the simulation, maximum amplitudes for MC movements are selected as to obtain roughly a 40% acceptance rate.
Once a movement in helical coordinates is accepted by Metropolis test, the corresponding Cartesian structure of the fiber is generated using an adaptation of X3DNA for VIDEO visualization using JMOL java scripts in the HTML page. Basic manipulation analysis of the trajectories and structure (rotations, translations, distance measurements, ...) are allowed by the JMOL interface.
The server shows an animation of the DNA dynamics in water solution at 25 °C. The dynamics of proteins are not computed and the segment of DNA binding the protein stays rigid. The number of steps of the Montecarlo algorithm is proportional to the number of non-rigid dinucleotides in DNA (100,000 x number of flexible dinucleotides). As Jmol is not able to reproduce large animations, not all the steps of the Montecarlo algorithm are shown in the animation.
This is a sample movie using the actual software that we run to animate the DNA, please wait some seconds until it has been loaded completely. You should see some DNA moving.
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.