title   
  

A tabu search approach for the NMR protein structure-based assignment problem

Çavuşlar, Gizem and Çatay, Bülent and Apaydın, Serkan Mehmet (2011) A tabu search approach for the NMR protein structure-based assignment problem. [Working Paper / Technical Report] Sabanci University ID:10.5900/SU_FENS_WP.2011.18983

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Abstract

Nuclear Magnetic Resonance (NMR) Spectroscopy is an experimental technique which exploits the magnetic properties of specific nuclei and enables the study of proteins in solution. The key bottleneck of NMR studies is to map the NMR peaks to corresponding nuclei, also known as the assignment problem. Structure Based Assignment (SBA) is an approach to solve this computationally challenging problem by using prior information about the protein obtained from a homologous structure. NVR-BIP used the Nuclear Vector Replacement (NVR) framework to model SBA as a binary integer programming problem. In this paper, we prove that this problem is NP-hard and propose a tabu search algorithm (NVR-TS) equipped with a guided perturbation mechanism to efficiently solve it. NVRTS uses a quadratic penalty relaxation of NVR-BIP where the violations in the Nuclear Overhauser Effect constraints are penalized in the objective function. Experimental results indicate that our algorithm finds the optimal solution on NVR-BIP’s data set which consists of 7 proteins with 25 templates (31 to 126 residues). Furthermore, it achieves relatively high assignment accuracies on two additional large proteins, MBP and EIN (348 and 243 residues, respectively), which NVR-BIP failed to solve. The executable and the input files are available for download at http://people.sabanciuniv.edu/catay/NVRTS/NVR-TS.html

Item Type:Working Paper / Technical Report
Additional Information:SU_FENS_2011/0001
Uncontrolled Keywords:Automated NMR assignments, tabu search, NMR Structural Biology, Structural bioinformatics
Subjects:T Technology > TA Engineering (General). Civil engineering (General) > TA164 Bioengineering
T Technology > T Technology (General) > T055.4-60.8 Industrial engineering. Management engineering
T Technology > T Technology (General) > T055.4-60.8 Industrial engineering. Management engineering > T57.6-57.97 Operations research. Systems analysis
ID Code:18983
Deposited By:Bülent Çatay
Deposited On:07 May 2012 12:26
Last Modified:07 May 2012 12:26

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