Fibonacci heaps and their uses in improved network optimization algorithms
Journal of the ACM (JACM)
Faster scaling algorithms for network problems
SIAM Journal on Computing
An efficient cost scaling algorithm for the assignment problem
Mathematical Programming: Series A and B
Protein structure determination using protein threading and sparse NMR data (extended abstract)
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
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
Automated Protein NMR Resonance Assignments
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
High-Throughput 3D Structural Homology Detection via NMR Resonance Assignment
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
CISA: Combined NMR Resonance Connectivity Information Determination and Sequential Assignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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 assignment is one of the key steps in solving an NMR protein structure. The assignment process is tedious and time-consuming, and although many computer programs can assist the assignment process, several NMR labs still do the assignments manually or semimanually for quality reasons. The authors present a new computational framework for automating the assignment process, particularly for backbone resonance peak assignment. They formulate the assignment problem as a constrained weighted bipartite matching problem, which provides a natural framework for incorporating all available information into the assignment process. Although they can show that the constrained bipartite matching problem, in the most general situation, is NP-hard, they developed a rigorous algorithm for solving the problem. For practical data, the algorithm runs fast, taking advantage of the discerning power of their scoring scheme and ruling out a vast majority of bad individual assignments in a preprocessing step. They have implemented the algorithm and tested it on four proteins with both real and simulated NMR peaks. Their results show that when 75 percent of all the connectivities between NMR peaks are identified with simulated data, their assignment results will be close to or reach 100 percent accuracy. With the realistic connectivity information obtained from experimental peaks, their program can assign majority of the peaks correctly.