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Bio-Algorithms and Med-Systems

Editor-in-Chief: Roterman-Konieczna , Irena


CiteScore 2018: 0.29

SCImago Journal Rank (SJR) 2018: 0.129
Source Normalized Impact per Paper (SNIP) 2018: 0.324

ICV 2018: 120.80

Online
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1896-530X
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Measurement of Hydrophobicity Distribution in Proteins � Complete Redundant Protein Data Bank.

Kinga Sałapa
  • Jagiellonian University Medical College, Department of Bioinformatics and Telemedicine, Łazarza 16, 31-530 Kraków, Poland
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/ Barbara Kalinowska
  • Jagiellonian University Medical College, Department of Bioinformatics and Telemedicine, Łazarza 16, 31-530 Kraków, Poland
  • Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, Reymonta 4, 30-059 Kraków, Poland
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  • De Gruyter OnlineGoogle Scholar
/ Tomasz Jadczyk
  • University of Science and Technology, Academic Computer Center Cyfronet AGH, Nawojki 11, 30-950, Kraków, Poland
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/ Irena Roterman
  • Jagiellonian University Medical College, Department of Bioinformatics and Telemedicine, Łazarza 16, 31-530 Kraków, Poland
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Abstract

The divergence entropy: O/T and O/R measuring the distance between observed/theoretical and observed/random distributions was applied to identify the category of protein structures in respect to the hydrophobic core in protein molecules. The naive interpretation was applied treating the proteins of O/T < O/R as the molecules of hydrophobic core accordant with the theoretically assumed. The proteins of O/T > O/R are treated as representing the hydrophobic core not accordant with the assumed one. The large scale computing was performed (PDB data set) to reveal whether other than simple inequality relation should be used for this identification. The cluster analysis was applied to identify the relation O/T versus O/R as the discrimination factor to classify the category of proteins in respect to their structural form of hydrophobic core.

Keywords: cluster analysis; divergence entropy; protein structure; hydrophobic core

Artikelinformationen

Erhalten: 06.03.2012

Revidiert: 23.03.2012

Angenommen: 26.03.2012

Erschienen im Druck:


Quellenangabe: Bio-Algorithms and Med-Systems BAMS, Band 8, Seiten 195–206, ISSN (Online) 1896-530X, ISSN (Print) 1895-9091, DOI: https://doi.org/10.2478/bams-2012-0018.

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©Jagiellonian University, Medical College, Kraków, Poland, 2012.

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