PREDICTOR: A Web-Based Tool for the Prediction of Atomic Structure from Sequence for Double Helical DNA with up to 150 Base Pairs

Article type: Research Article

Authors: Farwer, Jochen | Packer, Martin J. | Hunter, Christopher A.

Affiliations: Department of Chemistry, University of Sheffield, Western Bank, S10 2TN Sheffield, UK

Note: [] Corresponding author. E-mail: j.farwer@shef.ac.uk

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

Journal: In Silico Biology, vol. 7, no. 6, pp. 595-600, 2007