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A combinatorial model of molecular conformational space that was previously developed, had the drawback that structures could not be properly embedded because it lacked explicit rotational symmetry. The problem can be circumvented by sorting the elementary 3D components of a molecular system into a finite set of classes that can be separately embedded. This… (More)

Protein structures can be encoded into binary sequences (Gabarro-Arpa et al., Comput Chem 2000;24:693-698) these are used to define a Hamming distance in conformational space: the distance between two different molecular conformations is the number of different bits in their sequences. Each bit in the sequence arises from a partition of conformational space… (More)

— In the first work of this series [1] it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the espace into a hierarchical set of cells that can be encoded by the face lattice poset of the arrangement. The model however, lacked explicit… (More)

On the basis of empirical evidence from molecular dynamics simulations, molecular conformational space can be described by means of a partition of central conical regions (cells) characterized by the dominance relations between cartesian coordinates. This work presents a geometric and combinatorial description of the cell arrangement which is polar to a… (More)

In previous works it was shown that the 3 × N-dimensional conformational space of a molecular system could be divided into a number of cells, and from data sampled from molecular dynamics simulations it was possible to build a structure: the graph of cells, encoding the set of cells in conformational space that the system visits in its thermal wandering.… (More)

For a series of wild type and mutated eucaryotic gene prelude sequences (mainly "promoters" of SV40 early gene (Benoist and Chambon, Nature 290, 304 (1981); Moreau et al., Nuc. Acids Res. 9, 6047 (1982)) and of Herpes Simplex Virus TK gene (McKnight and Kingsbury, Science 217, 316 (1982)), in vivo promoter activity and local stability (denaturability) have… (More)

In a previous work [physics/061108v2], it was shown that the volume spanned by a molecular system in its conformational space can be effectively bounded by a polyhedral cone, this cone is described by means of a simple combinatorial formula. On the other hand it was constructed a transversal graph structure encoding the region of conformational space… (More)

In a previous work (Gabarro-Arpa, J. Math. Chem. 42 (2006) 691-706) a procedure was decribed for dividing the 3 × N-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the building of a combinatorial structure from data sampled in molecular dynamics trajectories: the graph of cells or G, encoding… (More)