A Combinatorial Enumeration of Distances for Calculating Energy in Molecular Conformational Space

TL;DR

This paper introduces a combinatorial method to enumerate and analyze molecular conformations in 3D space using dominance partition sequences, enabling energy calculations within a structured lattice framework.

Contribution

It presents a novel approach to encode protein conformations and compute their mean energy through combinatorial algorithms on a structured lattice.

Findings

Efficient enumeration of conformations compatible with DPS

Graph-based structure for conformational analysis

Algorithm for mean energy computation in conformational cells

Abstract

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.