Euclidean distance geometry and applications

L Liberti, C Lavor, N Maculan, A Mucherino - SIAM review, 2014 - SIAM
Euclidean distance geometry is the study of Euclidean geometry based on the concept of
distance. This is useful in several applications where the input data consist of an incomplete …

Recent advances on the discretizable molecular distance geometry problem

C Lavor, L Liberti, N Maculan, A Mucherino - European Journal of …, 2012 - Elsevier
The Molecular Distance Geometry Problem (MDGP) consists in finding an embedding in R3
of a nonnegatively weighted simple undirected graph with the property that the Euclidean …

The discretizable molecular distance geometry problem

C Lavor, L Liberti, N Maculan, A Mucherino - Computational Optimization …, 2012 - Springer
Given a simple weighted undirected graph G=(V, E, d) with d: E→ ℝ+, the Molecular
Distance Geometry Problem (MDGP) consists in finding an embedding x: V→ ℝ 3 such …

Recent advances on the interval distance geometry problem

DS Gonçalves, A Mucherino, C Lavor… - Journal of Global …, 2017 - Springer
We discuss a discretization-based solution approach for a classic problem in global
optimization, namely the distance geometry problem (DGP). We focus our attention on a …

The interval Branch-and-Prune algorithm for the discretizable molecular distance geometry problem with inexact distances

C Lavor, L Liberti, A Mucherino - Journal of Global Optimization, 2013 - Springer
Abstract The Distance Geometry Problem in three dimensions consists in finding an
embedding in R^ 3 of a given nonnegatively weighted simple undirected graph such that …

The discretizable distance geometry problem

A Mucherino, C Lavor, L Liberti - Optimization Letters, 2012 - Springer
We introduce the discretizable distance geometry problem in R^ 3 (DDGP 3), which consists
in a subclass of instances of the Distance Geometry Problem for which an embedding in R …

Discretization orders for distance geometry problems

C Lavor, J Lee, A Lee-St. John, L Liberti… - Optimization …, 2012 - Springer
Given a weighted, undirected simple graph G=(V, E, d)(where d: E → R _+), the distance
geometry problem (DGP) is to determine an embedding x: V → R^ K such that ∀ {i, j\} ∈ E\; …

[HTML][HTML] An algorithm to enumerate all possible protein conformations verifying a set of distance constraints

A Cassioli, B Bardiaux, G Bouvier, A Mucherino… - BMC …, 2015 - Springer
Background The determination of protein structures satisfying distance constraints is an
important problem in structural biology. Whereas the most common method currently …

[HTML][HTML] On the number of realizations of certain Henneberg graphs arising in protein conformation

L Liberti, B Masson, J Lee, C Lavor… - Discrete Applied …, 2014 - Elsevier
Several application fields require finding Euclidean coordinates consistent with a set of
distances. More precisely, given a simple undirected edge-weighted graph, we wish to find a …

[HTML][HTML] Minimal NMR distance information for rigidity of protein graphs

C Lavor, L Liberti, B Donald, B Worley… - Discrete Applied …, 2019 - Elsevier
Abstract Nuclear Magnetic Resonance (NMR) experiments provide distances between
nearby atoms of a protein molecule. The corresponding structure determination problem is …