Protein Threading: From Mathematical Models to Parallel Implementations

Authors:
Rumen Andonov;Stefan Balev;Nicola Yanev
Affiliations:
LAMIH/ROI, Université de Valenciennes, Le Mont Houy, 59313 Valenciennes Cedex 9, France;Laboratoire d'Informatique du Havre EA 3219, Université du Havre, 25 rue Philippe Lebon, BP 540, 76058 Le Havre cedex, France;Faculty of Mathematics and Computer Science, University of Sofia, 5, J. Bouchier str., 1126 Sofia, Bulgaria
Venue:
INFORMS Journal on Computing
Year:
2004

Citing 3
Cited 4

On the approximation of protein threading

Theoretical Computer Science - Special issue: Genome informatics
Solving the Protein Threading Problem in Parallel

IPDPS '03 Proceedings of the 17th International Symposium on Parallel and Distributed Processing
Computational challenges in structural and functional genomics

IBM Systems Journal - Deep computing for the life sciences

FROST: Revisited and Distributed

IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 7 - Volume 08
Lagrangian approaches for a class of matching problems in computational biology

Computers & Mathematics with Applications
An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem

WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Optimal protein threading by cost-splitting

WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics

Quantified Score

Hi-index	0.00

Visualization

Abstract

This paper presents a new network-flow formulation for the problem of predicting 3D protein structures using threading. Several integer-programming models based on this formulation are proposed and compared. These models allow for an efficient decomposition and for the application of a parallel branch-and-cut algorithm, significantly reducing the running time. The efficiency of our approach has been confirmed by extensive computational experiments.