Knowledge-based prediction of DNA atomic structure from nucleic sequence.
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 RMSE around 0.5 A for the translational conformational coordinates, and around 5 degrees for the rotational. For the estimation of the nucleic base non-hydrogen atom coordinates the RMSE is around 1.1 A. The knowledge-based method outperformed a technique based on genetic algorithms in the prediction of B-DNA structures.
Araúzo-Bravo
Marcos J
MJ
Department of Biosciences and Bioinformatics, Kyushu Institute of Technology, 1-1 Kawazu, Iizuka, Fukuoka 820-8502, Japan. marara@bse.kyutech.ac.jp
Sarai
Akinori
A
D001483:Base Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D009690:Nucleic Acid Conformation
D004247:DNA