Abstract
A simple knowledge-based method for DNA atomic structure prediction from nucleic sequence is presented. We used free B-DNA crystal structures to estimate the distribution of trinucleotide base pairs and tetranucleotide base-pair steps conformational coordinates. We used these distributions as a basis to predict the 3D position of the non-hydrogen atoms of the nucleic bases of any arbitrary DNA sequence of any length. The only constraint imposed was that the structure is a B-DNA one with Watson-Crick complementary base pairs. The method was tested on not seen DNA structures with sequence lengths varying from 6bp to 12bp. The obtained predictions have RNISE around 0.5 Å for the translational conformational coordinates, and around 5° for the rotational. For the estimation of the nucleic base non-hydrogen atom coordinates the RMSE is around 1.1 Å. The knowledge-based method outperformed a technique based on genetic algorithms in the prediction of B-DNA structures.
