Evolutionary approach to NOE paths assignment in RNA structure elucidation

Błażewicz, Jacek; Szachniuk, Marta; Wójtowicz, Adam

doi:10.1109/cibcb.2004.1393955

Cited by 4 publications

(4 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recently, the correlation signals occurring between the nuclei of RNA molecule during Nuclear Magnetic Resonance (NMR) experiments have been represented with an edge-colored graph model [2,10,11,42,43]. NMR experiments are used in the determination and analysis of protein and nucleic acid structures, they often complement in silico prediction [12] and are applied in the validation of computed molecular models [48].…”

Section: Applications Of Oclpmentioning

confidence: 99%

“…The longest orderly colored simple path along the vertices of G is the reconstruction of a transfer pathway between the cross-peaks in the spectrum, and -respectively -a magnetization transfer between the nuclei of RNA molecule. Similarly, in [2,10,42], the problem of NMR signal assignment is studied for the two-dimensional spectra. The search space in this case can be modelled as 2-edge-colored graph, and the solution to the 2D assignment problem is the longest alternating simple path.…”

Section: Applications Of Oclpmentioning

confidence: 99%

See 1 more Smart Citation

The Orderly Colored Longest Path Problem – a survey of applications and new algorithms

et al. 2013

View full text Add to dashboard Cite

A concept of an Orderly Colored Longest Path (OCLP) refers to the problem of finding the longest path in a graph whose edges are colored with a given number of colors, under the constraint that the path follows a predefined order of colors. The problem has not been widely studied in the previous literature, especially for more than two colors in the color arrangement sequence. The recent and relevant application of OCLP is related to the interpretation of Nuclear Magnetic Resonance experiments for RNA molecules. Besides, an employment of this specific graph model can be found in transportation, games, and grid graphs. OCLP models the relationships between consecutive edges of the path, thus it appears very useful in representing the real problems with specific ties between their components. In the paper, we show OCLP's correlation with similar issues known in graph theory. We describe the applications, three alternative models and new integer programming algorithms to solve OCLP. They are formulated by means of max flow problems in a directed graph with packing constraints over certain partitions of nodes. The methods are compared in a computational experiment run for a set of randomly generated instances.

show abstract

Section: Applications Of Oclpmentioning

confidence: 99%

Section: Applications Of Oclpmentioning

confidence: 99%

The Orderly Colored Longest Path Problem – a survey of applications and new algorithms

et al. 2013

View full text Add to dashboard Cite

show abstract

“…Such experiments are widely used in structural molecular biology to determine three-dimensional shapes of molecules, to analyze their conformations (in vitro NMR) or to track the movements of molecules (in vivo NMR) [1,2]. NMR spectroscopy takes advantage of the fact, that many nuclei of biological molecules can produce their own magnetic fields.…”

Section: Introductionmentioning

confidence: 99%

“…Thus, a few methods have been developed especially for RNA assignment. They take advantage of exhaustive search [18,19], evolutionary algorithm [2,20], tabu [21,22] and beam search [23] strategies, and they have been applied to process the spectra recorded for regular duplex structures and small bulged duplexes. This paper is focused on the problem of resonance assignment considered for structures of irregular regions, generally understood as loops -the most common motifs occurring in RNA.…”

Section: Introductionmentioning

confidence: 99%

Assigning NMR spectra of irregular RNAs by heuristic algorithms

Szachniuk¹

2015

Bulletin of the Polish Academy of Sciences Technical Sciences

Self Cite

View full text Add to dashboard Cite

Abstract.Computer-aided analysis and preprocessing of spectral data is a prerequisite for any study of molecular structures by Nuclear Magnetic Resonance (NMR) spectroscopy. The data processing stage usually involves a considerable dedication of time and expert knowledge to cope with peak picking, resonance signal assignment and calculation of structure parameters. A significant part of the latter step is performed in an automated way. However, in peak picking and resonance assignment a multistage manual assistance is still essential. The work presented here is focused on the theoretical modeling and analyzing the assignment problem by applying heuristic approaches to the NMR spectra recorded for RNA structures containing irregular regions.

show abstract