Tuning interval branch-and-prune for protein structure determination

DOI10.1007/s10898-018-0635-0zbMath1422.92109OpenAlexW2792288784WikidataQ57077630 ScholiaQ57077630MaRDI QIDQ1756761

Leo Liberti, Florent Delhommel, Florence Cordier, Thérèse E. Malliavin, Nicolas Wolff, Michael Nilges, Benjamin Bardiaux, Bradley Worley, Carlile C. Lavor

Publication date: 21 December 2018

Published in: Journal of Global Optimization (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s10898-018-0635-0

zbMATH Keywords

distance geometryprotein structurenuclear magnetic resonancebranch-and-prune

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08)

Related Items

A note on the Cayley-Menger determinant and the molecular distance geometry problem, Unassigned distance geometry and molecular conformation problems, Improving the sampling process in the interval branch-and-prune algorithm for the discretizable molecular distance geometry problem, Pseudo-dihedral angles in proteins providing a new description of the Ramachandran map, A study on the covalent geometry of proteins and its impact on distance geometry, Exploration of conformations for an intrinsically disordered protein, Oriented conformal geometric algebra and the molecular distance geometry problem, Recent results on assigned and unassigned distance geometry with applications to protein molecules and nanostructures, NMR protein structure calculation and sphere intersections, On the estimation of unknown distances for a class of Euclidean distance matrix completion problems with interval data, Geometric algebra to describe the exact discretizable molecular distance geometry problem for an arbitrary dimension, iBP, A quantum approach to the discretizable molecular distance geometry problem

Uses Software

• CHARMM
• ARIA
• Xplor-NIH
• CNS

Cites Work

• Discretization orders for protein side chains
• Discretization vertex orders in distance geometry
• Clifford algebra and the discretizable molecular distance geometry problem
• Recent advances on the interval distance geometry problem
• The interval branch-and-prune algorithm for the discretizable molecular distance geometry problem with inexact distances
• The Discretizable Molecular Distance Geometry Problem seems Easier on Proteins
• Euclidean Distance Geometry and Applications