Wyniki wyszukiwania - BazTech

1

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

Zok T., Antczak M., Riedel M., Nebel D., Villmann T., Lukasiak P., Blazewicz J., Szachniuk M.

International Journal of Applied Mathematics and Computer Science

|

2015

|

Vol. 25, no. 3

689--700

EN

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 for sampling the space of RNA structures can reveal plausible conformational representatives useful for further analysis. Here, we present a machine learning-based approach to inspect the dataset of RNA three-dimensional structures and to create a library of nucleotide conformers. A median neural gas algorithm is applied to cluster nucleotide structures upon their trigonometric description. The clustering procedure is two-stage: (i) backbone- and (ii) ribose-driven. We show the resulting library that contains RNA nucleotide representatives over the entire data, and we evaluate its quality by computing normal distribution measures and average RMSD between data points as well as the prototype within each cluster.

2

Assigning NMR spectra of irregular RNAs by heuristic algorithms

Szachniuk M.

Bulletin of the Polish Academy of Sciences. Technical Sciences

|

2015

|

Vol. 63, nr 1

329--338

EN

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.

3

Cerberus: A New Information Retrieval Tool for Marine Metagenomics

Radom M., Kottmann R., Rybarczyk A., Formanowicz P., Szachniuk M., Glöckner F. O., Błażewicz J.

Foundations of Computing and Decision Sciences

|

2010

|

Vol. 35, No. 2

107-126

EN

The number of papers published every year in scientific journals is growing tremendously, especially in biological sciences. Keeping the track of a given branch of science is therefore a difficult task. This was one of the reasons for developing the classification tool we called Cerberus. The classification categories may correspond to some areas of research defined by the user. We have used the tool to classify papers as containing marine metagenomic, terrestrial metagenomic or non-metagenomic information. Cerberus is based on special filters using weighted domain vocabularies. Depending on the number of occurrences of the keywords from the vocabularies in the paper, the program classifies the paper to a predefined category. This classification can precede the information extraction since it can reduce the number of papers to be analyzed. Classification of papers using the method we propose results in an accurate and precise result set of articles that are relevant to the scientist. This can reduce the resources needed to find the data required in ones field of studies.

4

Evolutionary algorithm for a reconstruction of NOE paths in NMR spectra of RNA chains

Błażewicz J., Szachniuk M., Wojtowicz A.

Bulletin of the Polish Academy of Sciences. Technical Sciences

|

2004

|

Vol. 52, nr 3

221-230

EN

Resonance-assignment remains one of the hardest stages in RNA tertiary structure determination with the use of Nuclear Magnetic Resonanse spectroscopy. We propose an evolutionary algorithm being a tool for an automatization of the procedure. NOE pathway, which determines the assignments, is constructed during an analysis of possible connections between resonances within aromatic and anomeric region of 2D-NOESY spectra resulting from appropriate NMR experiments. Computational tests demonstrate the performance of the evolutionary algorithm as compared with the exact branch-and-cut procedure applied for the experimental and simulated spectral data for RNA molecules.