Carlile Lavor

Nilton Maia

Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

2022

A quantum approach to the discretizable molecular distance geometry problem.

[BibT_eX]

[DOI]

Franklin L. Marquezino

Andrês Oliveira

Renato Portugal

Quantum Inf. Process., 2022

Unassigned distance geometry and molecular conformation problems.

[BibT_eX]

[DOI]

J. Glob. Optim., 2022

Preface: special issue on optimization in distance geometry.

[BibT_eX]

[DOI]

Andrés D. Báez-Sánchez

J. Glob. Optim., 2022

Distance geometry and protein loop modeling.

[BibT_eX]

[DOI]

Rodrigo Labiak

J. Comput. Chem., 2022

Linear and geometric algebra approaches for sphere and spherical shell intersections in Rn.

[BibT_eX]

[DOI]

Rafael Alves

Leandro A. F. Fernandes

Expert Syst. Appl., 2022

2021

A conjecture on a continuous optimization model for the Golomb Ruler Problem.

[BibT_eX]

[DOI]

RAIRO Oper. Res., 2021

A note on the Cayley-Menger determinant and the Molecular Distance Geometry Problem.

[BibT_eX]

[DOI]

Inf. Sci., 2021

Orthogonality of isometries in the conformal model of the 3D space.

[BibT_eX]

[DOI]

José Luis Aragón

Graph. Model., 2021

An impossible utopia in distance geometry.

[BibT_eX]

[DOI]

CoRR, 2021

On the optimality of finding DMDGP symmetries.

[BibT_eX]

[DOI]

Comput. Appl. Math., 2021

Improving the sampling process in the interval Branch-and-Prune algorithm for the discretizable molecular distance geometry problem.

[BibT_eX]

[DOI]

Appl. Math. Comput., 2021

A New Algorithm for the <sup>K</sup>DMDGP Subclass of Distance Geometry Problems with Exact Distances.

[BibT_eX]

[DOI]

Algorithmica, 2021

Pseudo-dihedral Angles in Proteins Providing a New Description of the Ramachandran Map.

[BibT_eX]

[DOI]

Proceedings of the Geometric Science of Information - 6th International Conference, 2021

2020

A constrained interval approach to the generalized distance geometry problem.

[BibT_eX]

[DOI]

Optim. Lett., 2020

Preface: Special issue on distances in optimization and graphs dedicated to the memory of Michel Deza.

[BibT_eX]

[DOI]

Optim. Lett., 2020

The K-discretization and K-incident graphs for discretizable Distance Geometry.

[BibT_eX]

[DOI]

Optim. Lett., 2020

A new algorithm for the <sup>K</sup>DMDGP subclass of Distance Geometry Problems.

[BibT_eX]

[DOI]

CoRR, 2020

MD-jeep: a New Release for Discretizable Distance Geometry Problems with Interval Data.

[BibT_eX]

[DOI]

Franklin de Lima Marquezino

Proceedings of the 2020 Federated Conference on Computer Science and Information Systems, 2020

An Online Calculator for Qubits Based on Geometric Algebra.

[BibT_eX]

[DOI]

Proceedings of the Advances in Computer Graphics, 2020

2019

A Primer on Quantum Computing

[BibT_eX]

[DOI]

Renato Portugal

Springer Briefs in Computer Science, Springer, ISBN: 978-3-030-19065-1, 2019

A mathematical programming formulation for the Hartree-Fock problem on open-shell systems.

[BibT_eX]

[DOI]

Optim. Lett., 2019

Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2019

On the polynomiality of finding KDMDGP re-orders.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2019

Minimal NMR distance information for rigidity of protein graphs.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2019

Realizing Euclidean distance matrices by sphere intersection.

[BibT_eX]

[DOI]

Jorge Alencar

Discret. Appl. Math., 2019

2018

Tuning interval Branch-and-Prune for protein structure determination.

[BibT_eX]

[DOI]

J. Glob. Optim., 2018

A new algorithm for the small-field astrometric point-pattern matching problem.

[BibT_eX]

[DOI]

Cláudio P. Santiago

Sérgio Assunção Monteiro

Alberto Krone-Martins

J. Glob. Optim., 2018

A symmetry-based splitting strategy for discretizable distance geometry problems.

[BibT_eX]

[DOI]

Felipe Fidalgo

J. Glob. Optim., 2018

Recent results on assigned and unassigned distance geometry with applications to protein molecules and nanostructures.

[BibT_eX]

[DOI]

Simon J. L. Billinge

Ann. Oper. Res., 2018

2017

An Introduction to Distance Geometry applied to Molecular Geometry

[BibT_eX]

[DOI]

Tiago Mendonça da Costa

Springer Briefs in Computer Science, Springer, ISBN: 978-3-319-57182-9, 2017

Recent advances on the interval distance geometry problem.

[BibT_eX]

[DOI]

J. Glob. Optim., 2017

Feasibility check for the distance geometry problem: an application to molecular conformations.

[BibT_eX]

[DOI]

Int. Trans. Oper. Res., 2017

Calculating the possible conformations arising from uncertainty in the molecular distance geometry problem using constraint interval analysis.

[BibT_eX]

[DOI]

Tiago Mendonça da Costa

H. Bouwmeester

Inf. Sci., 2017

New Error Measures and Methods for Realizing Protein Graphs from Distance Data.

[BibT_eX]

[DOI]

Discret. Comput. Geom., 2017

Modeling the Molecular Distance Geometry Problem Using Dihedral Angles.

[BibT_eX]

[DOI]

Rafael Alves

Proceedings of the Bioinformatics Research and Applications - 13th International Symposium, 2017

Euclidean Distance Geometry - an Introduction.

[BibT_eX]

[DOI]

Springer undergraduate texts in mathematics and technology, Springer, ISBN: 978-3-319-60791-7, 2017

2016

A projected gradient method for optimization over density matrices.

[BibT_eX]

[DOI]

Márcia A. Gomes-Ruggiero

Optim. Methods Softw., 2016

Six mathematical gems from the history of distance geometry.

[BibT_eX]

[DOI]

Int. Trans. Oper. Res., 2016

Preface to the Special Issue on Many Faces of Distances.

[BibT_eX]

[DOI]

Int. Trans. Oper. Res., 2016

A note on the sum of the largest signless Laplacian eigenvalues.

[BibT_eX]

[DOI]

Bruno D. Amaro

Leonardo Silva de Lima

Carla Silva Oliveira

Nair Abreu

Electron. Notes Discret. Math., 2016

Open research areas in distance geometry.

[BibT_eX]

[DOI]

CoRR, 2016

Assigned and unassigned distance geometry: applications to biological molecules and nanostructures.

[BibT_eX]

[DOI]

Simon J. L. Billinge

4OR, 2016

A New Approach to the Discretization of Multidimensional Scaling.

[BibT_eX]

[DOI]

Proceedings of the 2016 Federated Conference on Computer Science and Information Systems, 2016

Advances on the Geometric Algebra approach to the Discretizable Molecular Distance Geometry Problem (DMDGP).

[BibT_eX]

[DOI]

Rafael Alves

Cipriano de Souza

Proceedings of the Short Paper Proceedings of the 33rd Computer Graphics International, Heraklion, Greece, June 28, 2016

2015

An algorithm for realizing Euclidean distance matrices.

[BibT_eX]

[DOI]

Electron. Notes Discret. Math., 2015

Preface.

[BibT_eX]

[DOI]

Rosiane de Freitas Rodrigues

Discret. Appl. Math., 2015

Discretization vertex orders in distance geometry.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2015

An algorithm to enumerate all possible protein conformations verifying a set of distance constraints.

[BibT_eX]

[DOI]

BMC Bioinform., 2015

Distance Geometry on the Sphere.

[BibT_eX]

[DOI]

Grzegorz Swirszcz

Proceedings of the Discrete and Computational Geometry and Graphs - 18th Japan Conference, 2015

2014

BetaMDGP: Protein Structure Determination Algorithm Based on the Beta-complex.

[BibT_eX]

[DOI]

Trans. Comput. Sci., 2014

Euclidean Distance Geometry and Applications.

[BibT_eX]

[DOI]

SIAM Rev., 2014

Global convergence of diluted iterations in maximum-likelihood quantum tomography.

[BibT_eX]

[DOI]

Márcia A. Gomes-Ruggiero

Quantum Inf. Comput., 2014

A new hybrid classical-quantum algorithm for continuous global optimization problems.

[BibT_eX]

[DOI]

Pedro C. S. Lara

Renato Portugal

J. Glob. Optim., 2014

Discretization orders for protein side chains.

[BibT_eX]

[DOI]

J. Glob. Optim., 2014

On the number of realizations of certain Henneberg graphs arising in protein conformation.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2014

An adaptive branching scheme for the Branch & Prune algorithm applied to Distance Geometry.

[BibT_eX]

[DOI]

Proceedings of the 2014 Federated Conference on Computer Science and Information Systems, 2014

A Combinatorial Approach to Multidimensional Scaling.

[BibT_eX]

[DOI]

Jorge Alencar

Tibérius O. Bonates

Proceedings of the 2014 IEEE International Congress on Big Data, Anchorage, AK, USA, June 27, 2014

2013

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

[BibT_eX]

[DOI]

J. Glob. Optim., 2013

A discrete search algorithm for finding the structure of protein backbones and side chains.

[BibT_eX]

[DOI]

Silas Sallaume

Simone de Lima Martins

Luiz Satoru Ochi

Warley Gramacho Da Silva

Int. J. Bioinform. Res. Appl., 2013

Solving the molecular distance geometry problem with inaccurate distance data.

[BibT_eX]

[DOI]

BMC Bioinform., 2013

The integration of Clifford Algebra in the iBP algorithm for the DMDGP.

[BibT_eX]

[DOI]

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013

Counting the Number of Solutions of KDMDGP Instances.

[BibT_eX]

[DOI]

Proceedings of the Geometric Science of Information - First International Conference, 2013

Energy-based Pruning Devices for the BP Algorithm applied to Distance Geometry.

[BibT_eX]

[DOI]

Proceedings of the 2013 Federated Conference on Computer Science and Information Systems, 2013

Solving the Discretizable Molecular Distance Geometry Problem by Multiple Realization Trees.

[BibT_eX]

[DOI]

Pedro Nucci

Loana Tito Nogueira

Proceedings of the Distance Geometry: Theory, Methods, and Applications, 2013

The Discretizable Molecular Distance Geometry Problem seems Easier on Proteins.

[BibT_eX]

[DOI]

Proceedings of the Distance Geometry: Theory, Methods, and Applications, 2013

2012

Local solutions of maximum likelihood estimation in quantum state tomography.

[BibT_eX]

[DOI]

Márcia A. Gomes-Ruggiero

Osvaldo Jiménez Farias

P. H. Souto Ribeiro

Quantum Inf. Comput., 2012

The discretizable distance geometry problem.

[BibT_eX]

[DOI]

Optim. Lett., 2012

Discretization orders for distance geometry problems.

[BibT_eX]

[DOI]

Optim. Lett., 2012

Exploiting Symmetry Properties of the Discretizable molecular Distance Geometry Problem.

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 2012

Recent advances on the Discretizable Molecular Distance Geometry Problem.

[BibT_eX]

[DOI]

Eur. J. Oper. Res., 2012

The discretizable molecular distance geometry problem.

[BibT_eX]

[DOI]

Comput. Optim. Appl., 2012

A Parallel BP Algorithm for the Discretizable Distance Geometry Problem.

[BibT_eX]

[DOI]

Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012

On suitable orders for discretizing Molecular Distance Geometry Problems related to protein side chains.

[BibT_eX]

[DOI]

Virginia Costa

Proceedings of the Federated Conference on Computer Science and Information Systems, 2012

2011

Hyperbolic smoothing and penalty techniques applied to molecular structure determination.

[BibT_eX]

[DOI]

Oper. Res. Lett., 2011

On the computation of protein backbones by using artificial backbones of hydrogens.

[BibT_eX]

[DOI]

J. Glob. Optim., 2011

Molecular distance geometry methods: from continuous to discrete.

[BibT_eX]

[DOI]

Int. Trans. Oper. Res., 2011

A note on "A branch-and-prune algorithm for the molecular distance geometry problem".

[BibT_eX]

[DOI]

Int. Trans. Oper. Res., 2011

Polynomial cases of the Discretizable Molecular Distance Geometry Problem

[BibT_eX]

[DOI]

CoRR, 2011

Influence of Pruning Devices on the Solution of Molecular Distance Geometry Problems.

[BibT_eX]

[DOI]

Proceedings of the Experimental Algorithms - 10th International Symposium, 2011

Branch-and-Prune trees with bounded width.

[BibT_eX]

[DOI]

Proceedings of the 10th Cologne-Twente Workshop on graphs and combinatorial optimization. Extended Abstracts, 2011

On the Number of Solutions of the Discretizable Molecular Distance Geometry Problem.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Optimization and Applications, 2011

A symmetry-driven BP algorithm for the Discretizable Molecular Distance Geometry Problem.

[BibT_eX]

[DOI]

Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011

2010

MD-jeep: An Implementation of a Branch and Prune Algorithm for Distance Geometry Problems.

[BibT_eX]

[DOI]

Proceedings of the Mathematical Software, 2010

On the solution of molecular distance geometry problems with interval data.

[BibT_eX]

[DOI]

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010

A parallel version of the Branch & Prune algorithm for the Molecular Distance Geometry Problem.

[BibT_eX]

[DOI]

Proceedings of the 8th ACS/IEEE International Conference on Computer Systems and Applications, 2010

2009

Molecular Distance Geometry Problem.

[BibT_eX]

[DOI]

Proceedings of the Encyclopedia of Optimization, Second Edition, 2009

Double variable neighbourhood search with smoothing for the molecular distance geometry problem.

[BibT_eX]

[DOI]

J. Glob. Optim., 2009

Reformulation in mathematical programming: An application to quantum chemistry.

[BibT_eX]

[DOI]

Marco Antonio Chaer Nascimento

Discret. Appl. Math., 2009

On a discretizable subclass of instances of the molecular distance geometry problem.

[BibT_eX]

[DOI]

Proceedings of the 2009 ACM Symposium on Applied Computing (SAC), 2009

Computing artificial backbones of hydrogen atoms in order to discover protein backbones.

[BibT_eX]

[DOI]

Proceedings of the International Multiconference on Computer Science and Information Technology, 2009

Comparisons between an exact and a metaheuristic algorithm for the molecular distance geometry problem.

[BibT_eX]

[DOI]

Proceedings of the Genetic and Evolutionary Computation Conference, 2009

The Molecular Distance Geometry Problem Applied to Protein Conformations.

[BibT_eX]

[DOI]

Proceedings of the 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization, 2009

2008

A Branch-and-Prune algorithm for the Molecular Distance Geometry Problem.

[BibT_eX]

[DOI]

Ricardo dos Santos Carvalho

Int. Trans. Oper. Res., 2008

Extending the geometric build-up algorithm for the molecular distance geometry problem.

[BibT_eX]

[DOI]

Fábio Protti

Inf. Process. Lett., 2008

A continuous variable neighborhood search heuristic for finding the three-dimensional structure of a molecule.

[BibT_eX]

[DOI]

Eur. J. Oper. Res., 2008

2005

A GA-Simplex Hybrid Algorithm for Global Minimization of Molecular Potential Energy Functions.

[BibT_eX]

[DOI]

Helio J. C. Barbosa

Fernanda M. P. Raupp

Ann. Oper. Res., 2005

2004

A Function to Test Methods Applied to Global Minimization of Potential Energy of Molecules.

[BibT_eX]

[DOI]