An efficient cost scaling algorithm for the assignment problem
Mathematical Programming: Series A and B
Computing in Science and Engineering
Improved Approximation Algorithms for NMR Spectral Peak Assignment
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Approximation algorithms for NMR spectral peak assignment
Theoretical Computer Science
An Efficient Branch-and-Bound Algorithm for the Assignment of Protein Backbone NMR Peaks
CSB '02 Proceedings of the IEEE Computer Society Conference on Bioinformatics
An approximation algorithm for a bottleneck traveling salesman problem
Journal of Discrete Algorithms
An approximation algorithm for a bottleneck traveling salesman problem
CIAC'06 Proceedings of the 6th Italian conference on Algorithms and Complexity
RIBRA–an error-tolerant algorithm for the NMR backbone assignment problem
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
| Hi-index | 0.00 |
NMR resonance peak assignment is one of the key stepsin solving an NMR protein structure. The assignment processlinks resonance peaks to individual residues of thetarget protein sequence, providing the prerequisite for establishingintra- and inter-residue spatial relationships betweenatoms. The assignment process is tedious and time-consuming,which could take many weeks. Though thereexist a number of computer programs to assist the assignmentprocess, many NMR labs are still doing the assignmentsmanually to ensure quality. This paper presents (1)a new scoring system for mapping spin systems to residues,(2) an automated adjacency information extraction procedurefrom NMR spectra, and (3) a very fast assignment algorithmbased on our previous proposed greedy filteringmethod and a maximum matching algorithm to automatethe assignment process. The computational tests on 70 instancesof (pseudo) experimental NMR data of 14 proteinsdemonstrate that the new score scheme has much better discerningpower with the aid of adjacency information betweenspin systems simulated across various NMR spectra.Typically, with automated extraction of adjacency information,our method achieves nearly complete assignments formost of the proteins. The experiment shows very promisingperspective that the fast automated assignment algorithmtogether with the new score scheme and automated adjacencyextraction may be ready for practical use.