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تسجيل مستخدم جديدA Combinatorial Enumeration of Distances for Calculating Energy in Molecular Conformational Space
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Jacques Gabarro-Arpa
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In previous works it was shown that protein 3D-conformations could be encoded into discrete sequences called dominance partition sequences (DPS), that generated a linear partition of molecular conformational space into regions of molecular conformations that have the same DPS. In this work we describe procedures for building in a cubic lattice the set of 3D-conformations that are compatible with a given DPS. Furthermore, this set can be structured as a graph upon which a combinatorial algorithm can be applied for computing the mean energy of the conformations in a cell.
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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 characterized by the dominance relations between cartesian coordinates. This wo
rk presents a geometric and combinatorial description of this structure.
In a previous work arXiv:physics/0611108v2, 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
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