Related papers: The Discretizable Molecular Distance Geometry Prob…
The fundamental inverse problem in distance geometry is the one of finding positions from inter-point distances. The Discretizable Molecular Distance Geometry Problem (DMDGP) is a subclass of the Distance Geometry Problem (DGP) whose search…
The Discretizable Molecular Distance Geometry Problem (DMDGP) consists in a subclass of the Molecular Distance Geometry Problem for which an embedding in ${\mathbb{R}^3}$ can be found using a Branch & Prune (BP) algorithm in a discrete…
The Discretizable Molecular Distance Geometry Problem (DMDGP) aims to determine the three-dimensional protein structure using distance information from nuclear magnetic resonance experiments. The DMDGP has a finite number of candidate…
Distance Geometry plays a central role in determining protein structures from Nuclear Magnetic Resonance (NMR) data, a task known as the Molecular Distance Geometry Problem (MDGP). A subclass of this problem, the Discretizable Distance…
The Molecular Distance Geometry Problem (MDGP) is essential in structural biology, as it seeks to determine three-dimensional protein structures from partial interatomic distances. Its discretizable subclass (DMDGP) admits an exact…
The Distance Geometry Problem (DGP) seeks to find positions for a set of points in geometric space when some distances between pairs of these points are known. The so-called discretization assumptions allow to discretize the search space of…
Given an integer dimension K and a simple, undirected graph G with positive edge weights, the Distance Geometry Problem (DGP) aims to find a realization function mapping each vertex to a coordinate in K-dimensional space such that the…
The Generalized Discretizable Molecular Distance Geometry Problem is a distance geometry problems that can be solved by a combinatorial algorithm called ``Branch-and-Prune''. It was observed empirically that the number of solutions of YES…
The interval Distance Geometry Problem (iDGP) consists in finding a realization in $\mathbb{R}^K$ of a simple undirected graph $G=(V,E)$ with nonnegative intervals assigned to the edges in such a way that, for each edge, the Euclidean…
An important application of distance geometry to biochemistry studies the embeddings of the vertices of a weighted graph in the three-dimensional Euclidean space such that the edge weights are equal to the Euclidean distances between…
The Maximally Diverse Grouping Problem (MDGP) is the problem of assigning a set of elements to mutually disjoint groups in order to maximise the overall diversity between the elements. Because the MDGP is NP-complete, most studies have…
The Ordered Covering Problem (OCP) arises in the context of the Discretizable Molecular Distance Geometry Problem (DMDGP), where the ordering of pruning edges significantly impacts the performance of the SBBU algorithm for protein structure…
In this paper, we propose a fast and convergent algorithm to solve unassigned distance geometry problems (uDGP). Technically, we construct a novel quadratic measurement model by leveraging $\ell_0$-norm instead of $\ell_1$-norm in the…
Distance Geometry Problem (DGP) and Nonlinear Mapping (NLM) are two well established questions: Distance Geometry Problem is about finding a Euclidean realization of an incomplete set of distances in a Euclidean space, whereas Nonlinear…
The Euclidean distance geometry problem arises in a wide variety of applications, from determining molecular conformations in computational chemistry to localization in sensor networks. When the distance information is incomplete, the…
A fundamental problem in drug discovery is to design molecules that bind to specific proteins. To tackle this problem using machine learning methods, here we propose a novel and effective framework, known as GraphBP, to generate 3D…
For a graph $G=(V,E)$, a set $D\subseteq V$ is called a \emph{disjunctive dominating set} of $G$ if for every vertex $v\in V\setminus D$, $v$ is either adjacent to a vertex of $D$ or has at least two vertices in $D$ at distance $2$ from it.…
The problem of recovering the configuration of points from their partial pairwise distances, referred to as the Euclidean Distance Matrix Completion (EDMC) problem, arises in a broad range of applications, including sensor network…
A common starting point for drug design is to find small chemical groups or "fragments" that form interactions with distinct subregions in a protein binding pocket. The subsequent challenge is to assemble these fragments into a molecule…
High-dimensional PDEs have been a longstanding computational challenge. We propose to solve high-dimensional PDEs by approximating the solution with a deep neural network which is trained to satisfy the differential operator, initial…