Abstract: We announce the release of a web-based tool for DNA structure
prediction (PREDICTOR) which allows the calculation of atomic structures of
double-helical DNA with up to 150 Watson-Crick base pairs
(http://farwer.staff.shef.ac.uk/ PREDICTOR). The semi-empirical method uses
computational chemistry to extrapolate knowledge of sequence-dependent DNA
structure contained in the X-ray crystal structure database. The properties of
the base stacking interactions are treated theoretically, and an empirical
model is used to add the conformational constraints imposed by the backbone.
For DNA oligomers in the X-ray crystal structure database that were not used
for parameterisation of the model, the method distinguishes A and B form DNA
reasonably reliably, and the final structures are accurate to 2 å rmsd.
Simulation of a 150mer and a 494mer with experimentally confirmed bending
clearly reproduces the bending whereas the predicted structure of a random
150mer does not show any curvature. Calculation times are 90 seconds for an
octamer and 7 minutes for a 30mer.
Keywords: DNA conformation, DNA sequence-dependent structure, DNA atomic structure prediction, step parameters, DNA backbone conformation