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Your search keyword '"Piwowar, Piotr"' showing total 13 results
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13 results on '"Piwowar, Piotr"'

9. ExonVisualiser – application for visualization exon units in 2D and 3D protein structures

Author

Monika Piwowar, Porembski Krzysztof, and Piwowar Piotr

Subjects
Protein Data Bank (RCSB PDB), Exon visualisation, General Medicine, Computational biology, Biology, computer.software_genre, Protein tertiary structure, Exon unit identification in proteins, Exon, Protein structure, GenBank, Consensus sequence, Data mining, Gene, computer, Software, Sequence (medicine)
Abstract

UNLABELLED The web application oriented on identification and visualization of protein regions encoded by exons is presented. The Exon Visualiser can be used for visualisation on different levels of protein structure: at the primary (sequence) level and secondary structures level, as well as at the level of tertiary protein structure. The programme is suitable for processing data for all genes which have protein expressions deposited in the PDB database. The procedure steps implemented in the application: I) loading exons sequences and theirs coordinates from GenBank file as well as protein sequences: CDS from GenBank and aminoacid sequence from PDB II) consensus sequence creation (comparing amino acid sequences form PDB file with the CDS sequence from GenBank file) III) matching exon coordinates IV) visualisation in 2D and 3D protein structures. Presented web-tool among others provides the color-coded graphical display of protein sequences and chains in three dimensional protein structures which are correlated with the corresponding exons. AVAILABILITY http://149.156.12.53/ExonVisualiser/

Published
2012

11. Road Traffic Parameters Measuring System with Variable Structure

Author

Burnos, Piotr, Gajda, Janusz, Marszalek, Zbigniew, Piwowar, Piotr, Sroka, Ryszard, Stencel, Marek, and Zeglen, Tadeusz

Abstract

Road Traffic Parameters Measuring System with Variable StructureSystems of road traffic parameters measurement play a key role in the process of road traffic control, its supervision as well as in gathering and processing information for statistical purposes. Expectations of users of such systems mainly concern automation and provision of measurement continuity, possibility of selection of the measured road traffic parameters and high accuracy along with reliability of obtained results. In order to meet the requirements set for such systems, at the Department of Instrumentation and Measurement of the AGH University of Science and Technology in Cracow a new prototype system of road traffic parameters measurement - Traffic-1 - has been constructed. The innovativeness of the solution is manifested in the structure of the system that can be modified by the user adequately to current measurement needs and in the used algorithms of signals processing. The work contains a brief description of the constructed system with particular focus on the used innovations that are the result of many years of research work of the designers.

Published
2011
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12. Protein Conditioning for Binding Congo Red and Other Supramolecular Ligands

Author

Zemanek G, Jagusiak A, Rybarska J, Piwowar P, Chłopaś K, Roterman I, Roterman I, and Konieczny L

Abstract

Self-assembled organic compounds which form ribbon-like micellar clusters may attach themselves to proteins, penetrating in areas of low stability. Such complexation involves regions other than the protein’s natural binding site. The supramolecular ligand adheres to beta folds or random coils which become susceptible to complexation as a result of function-related structural changes – e.g. antibodies engaged in immune complexes or acute phase proteins. However, even seemingly unsusceptible helical proteins may bind Congo red if they include chameleon sequences (short peptide fragments capable of adopting different secondary conformations depending on environmental conditions). Examples of such proteins include hemoglobin and albumin. Complexation of supramolecular Congo red is often associated with increased fluorescence, indicating breakdown of ligand micelles in the complex. This phenomenon may be used in diagnostic tests., (Copyright 2018, The Author(s).)

Published
2018
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13. A tabular approach to the sequence-to-structure relation in proteins (tetrapeptide representation) for de novo protein design.

Author

Meus J, Brylinski M, Piwowar M, Piwowar P, Wiśniowski Z, Stefaniak J, Konieczny L, Surówka G, and Roterman I

Subjects
Amino Acid Sequence, Molecular Sequence Data, Protein Conformation, Protein Folding, Databases, Protein, Peptides chemistry, Proteins chemistry
Abstract

Background: Experimental observations classify the protein-folding process as a multi-step event. The backbone conformation has been experimentally recognized as responsible for the early-stage structural forms of a polypeptide. The sequence-to-structure and structure-to-sequence relation is critical for predicting protein structure. A contingency table representing this relation for tetrapeptides in their early-stage is presented. Their correlation seems to be essential in protein-folding simulation., Material/methods: The polypeptide chains of all the proteins in the Protein Data Bank were transformed into their early-stage structural forms. The tetrapeptide was selected as the structural unit. Tetrapetide sequences and structures were expressed by letter codes. The transformation of a contingency table of any size (here: 160,000x2401) to a 2x2 table performed for each non-zero cell of the original table allowed calculation of the rho-coefficient measuring the strength of the relation., Results: High values of the rho-coefficient extracted sequences of strong structural determinability and structures of high sequence selectivity. The web-site program to calculate the rho-coefficient ranking list was constructed to enable applying this method to any problem of contingency table analysis., Conclusions: The results revealed sequence-to-structure (and vice versa) correlation in early-stage folding. Surprisingly, the irregular structural forms of loops and bends appeared to be highly determined. Comparison of these results with another method based on information entropy revealed high accordance. The method oriented on interpretation of a large contingency table seems very useful especially for large-scale microarray analysis, a very popular technique in the post-genomic era.

Published
2006

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