Mar 28, 2008

A simple and fast heuristic for protein structure comparison

BMC Bioinformatics
D A PeltaMarcos Moreno Vega

Abstract

Protein structure comparison is a key problem in bioinformatics. There exist several methods for doing protein comparison, being the solution of the Maximum Contact Map Overlap problem (MAX-CMO) one of the alternatives available. Although this problem may be solved using exact algorithms, researchers require approximate algorithms that obtain good quality solutions using less computational resources than the formers. We propose a variable neighborhood search metaheuristic for solving MAX-CMO. We analyze this strategy in two aspects: 1) from an optimization point of view the strategy is tested on two different datasets, obtaining an error of 3.5%(over 2702 pairs) and 1.7% (over 161 pairs) with respect to optimal values; thus leading to high accurate solutions in a simpler and less expensive way than exact algorithms; 2) in terms of protein structure classification, we conduct experiments on three datasets and show that is feasible to detect structural similarities at SCOP's family and CATH's architecture levels using normalized overlap values. Some limitations and the role of normalization are outlined for doing classification at SCOP's fold level. We designed, implemented and tested.a new tool for solving MAX-CMO, based on a we...Continue Reading

  • References23
  • Citations15

References

  • References23
  • Citations15

Citations

Mentioned in this Paper

Heuristics
Bio-Informatics
Computer Programs and Programming
Tremor
Protein Conformation
Arthrogryposis Renal Dysfunction Cholestasis Syndrome
PHLPP1 wt Allele
Genetic Linkage
Silo (Dataset)
Sequence Analysis, Protein

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