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

Marta Szachniuk;  Maria Cristina De Cola;  Giovanni Felici;  Jacek Blazewicz — 2014

RAIRO - Operations Research - Recherche Opérationnelle

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...

Building the library of RNA 3D nucleotide conformations using the clustering approach

Tomasz Zok;  Maciej Antczak;  Martin Riedel;  David Nebel;  Thomas Villmann;  Piotr Lukasiak;  Jacek Blazewicz;  Marta Szachniuk — 2015

International Journal of Applied Mathematics and Computer Science

An increasing number of known RNA 3D structures contributes to the recognition of various RNA families and identification of their features. These tasks are based on an analysis of RNA conformations conducted at different levels of detail. On the other hand, the knowledge of native nucleotide conformations is crucial for structure prediction and understanding of RNA folding. However, this knowledge is stored in structural databases in a rather distributed form. Therefore, only automated methods...

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