Tuning interval Branch-and-Prune for protein structure determination

Bradley Worley (), Florent Delhommel (), Florence Cordier (), Thérèse E. Malliavin (), Benjamin Bardiaux (), Nicolas Wolff (), Michael Nilges (), Carlile Lavor () and Leo Liberti ()
Additional contact information
Bradley Worley: CNRS UMR3528, Centre de Bioinformatique, Biostatistique et Biologie Intégrative, CNRS USR3756, Institut Pasteu
Florent Delhommel: Institut Pasteur
Florence Cordier: Institut Pasteur
Thérèse E. Malliavin: CNRS UMR3528, Centre de Bioinformatique, Biostatistique et Biologie Intégrative, CNRS USR3756, Institut Pasteu
Benjamin Bardiaux: CNRS UMR3528, Centre de Bioinformatique, Biostatistique et Biologie Intégrative, CNRS USR3756, Institut Pasteu
Nicolas Wolff: Institut Pasteur
Michael Nilges: CNRS UMR3528, Centre de Bioinformatique, Biostatistique et Biologie Intégrative, CNRS USR3756, Institut Pasteu
Carlile Lavor: University of Campinas
Leo Liberti: LIX, École Polytechnique

Journal of Global Optimization, 2018, vol. 72, issue 1, No 7, 109-127

Abstract: Abstract The interval Branch and Prune (iBP) algorithm for obtaining solutions to the interval Discretizable Molecular Distance Geometry Problem (iDMDGP) has proven itself as a powerful method for molecular structure determination. However, substantial obstacles still must be overcome before iBP may be employed as a tractable general-purpose alternative to existing structure determination algorithms. This work introduces an iterative variant of the iBP algorithm that leverages existing knowledge of protein structures in order to reduce the size of the effective search space by many orders of magnitude. These improvements are included in a newly released implementation of the iBP software that aims to provide a solid platform for both research and application of the iDMDGP.

Keywords: Distance geometry; Protein structure; Nuclear magnetic resonance; Branch-and-Prune (search for similar items in EconPapers)
Date: 2018
References: View references in EconPapers View complete reference list from CitEc
Citations: View citations in EconPapers (3)

Downloads: (external link)
http://link.springer.com/10.1007/s10898-018-0635-0 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:spr:jglopt:v:72:y:2018:i:1:d:10.1007_s10898-018-0635-0

Ordering information: This journal article can be ordered from
http://www.springer. ... search/journal/10898

DOI: 10.1007/s10898-018-0635-0

Access Statistics for this article

Journal of Global Optimization is currently edited by Sergiy Butenko

More articles in Journal of Global Optimization from Springer
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().