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A Tabu Search Approach for the NMR Protein Structure-Based Assignment Problem
Nov.-Dec. 2012 (vol. 9 no. 6)
pp. 1621-1628
G. Cavuslar, Univ. of Wisconsin-Madison, Madison, WI, USA
B. Catay, Sabanci Univ., Istanbul, Turkey
M. S. Apaydin, Istanbul Sehir Univ., Istanbul, Turkey
Nuclear Magnetic Resonance (NMR) (Abbreviations used: NMR, Nuclear Magnetic Resonance; NOE, Nuclear Overhauser Effect; RDC, Residual Dipolar Coupling; PDB, Protein Data Bank; SBA, Structure-Based Assignments; NVR, Nuclear Vector Replacement; BIP, Binary Integer Programming; TS, Tabu Search; QAP, Quadratic Assignment Problem; ff2, the FF Domain 2 of human transcription elongation factor CA150 (RNA polymerase II C-terminal domain interacting protein); SPG, Streptococcal Protein G; hSRI, Human Set2-Rpb1 Interacting Domain; MBP, Maltose Binding Protein; EIN, Amino Terminal Domain of Enzyme I from Escherichia Coli; EM, expectation maximization) 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 (TS) algorithm (NVR-TS) equipped with a guided perturbation mechanism to efficiently solve it. NVR-TS 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 NVRBIP's data set which consists of seven 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/NVR-TS/NVR-TS.html.
Index Terms:
search problems,bioinformatics,biological NMR,cellular biophysics,enzymes,integer programming,microorganisms,molecular biophysics,molecular configurations,Overhauser effect,RNA,NVRBIP data set,Tabu search approach,NMR protein structure-based assignment problem,nuclear magnetic resonance,NOE,nuclear Overhauser effect,RDC,residual dipolar coupling,protein data bank,nuclear vector replacement,quadratic assignment problem,QAP,FF domain 2,human transcription elongation factor CA150,RNA polymerase II C-terminal domain interacting protein,SPG,streptococcal protein G,human Set2-Rpb1 interacting domain,MBP,maltose binding protein,EIN,amino terminal domain,enzyme I,Escherichia Coli,expectation maximization spectroscopy,magnetic properties,homologous structure,binary integer programming problem,Proteins,Nuclear magnetic resonance,Amino acids,Accuracy,Linear programming,Protons,Bioinformatics,structural bioinformatics,Automated NMR assignments,tabu search,NMR structural biology
Citation:
G. Cavuslar, B. Catay, M. S. Apaydin, "A Tabu Search Approach for the NMR Protein Structure-Based Assignment Problem," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 6, pp. 1621-1628, Nov.-Dec. 2012, doi:10.1109/TCBB.2012.122
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