3D molecular assembling of B-DNA sequences using nucleotides as building blocks
Unlike the current atomistic DNA models, this paper proposes a new 3D space-filling model for sequences of DNA base pairs using nucleotides, instead of atoms, as building blocks of DNA molecules. This nucleotide-based model is more scalable than the traditional atomistic model, and has the advantage that easily adapts to any topological conformation of DNA. Interestingly, this model also allows the building of the molecular surface of the DNA, either partly or entirely, as needed for energy computations in molecular applications. Moreover, it allows us to grasp the DNA shape at different levels of shape composition: atom, nucleotide, and DNA macromolecule as a whole. (c) 2012 Elsevier Inc. All rights reserved.
molecular surface dna geometry dna assembling dna shape composition dna base stacking dna conformations gaussian surface molecular modeling biomolecular visualization