Measurement of hydrophobicity distribution in proteins – non-redundant Protein Data Bank

• Autorzy: Sałapa K , Kalinowska B. , Jadczyk T. , Roterman I.
• Języki publikacji: EN

Abstrakty

EN

The cluster analysis is applied to the analysis of the data describing the status of protein structure in respect to hydrophobic core characteristics. The analysis revealed presence of two clusters distinguishing the proteins accordant with the “fuzzy oil drop” model and those which appear as discordant in respect to this model. The analysis was performed separately for chains treated as structural unit and for units defined according to IV-order (taking the functional protein complex). The characteristics of these two classification system appeared to differ in respect to number of proteins belonging to each of two clusters as well as relation between them.

Słowa kluczowe

EN

cluster analysis; data mining; decision tree

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2012
• Tom: Vol. 8, no. 3
• Strony: 327--337
• Opis fizyczny: Bibliogr. 7 poz., rys., tab., wykr.

Twórcy

autor

Sałapa K

• Department of Bioinformatics and Telemedicine – Jagiellonian University – Medical College, Lazarza 16, 31-530 Kraków, Poland

autor

Kalinowska B.

• Department of Bioinformatics and Telemedicine – Jagiellonian University – Medical College, Lazarza 16, 31-530 Kraków, Poland
• Faculty of Physics, Astronomy, Applied Computer Science, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland

autor

Jadczyk T.

• Academic Computer Center – Technical Academy of Science, Nawojki 11, 30-950 Kraków, Poland

autor

Roterman I.

• Department of Bioinformatics and Telemedicine – Jagiellonian University – Medical College, Lazarza 16, 31-530 Kraków, Poland

Bibliografia

• [1] Konieczny L, Bryliński M, Roterman I. (2006) Gauss-function-based model of hydrophobicity density in proteins. In Silico Biol. 6, 5-22.
• [2] Levitt M. A simplifed representation of protein conformations for rapid simulation of protein folding. J Mol Biol 104 (1976) 59–107
• [3] Nalewajski R.F. Information theory of molecular systems. Amsterdam [etc.]: Elsevier, 2006. ISBN 978-0-444-51966-5.
• [4] Sałapa K., Kalinowska B., Jadczyk T., Roterman I., (2012) Measurement of hydrophobicity distribution in proteins – complete redundant Protein Data Bank. Bio-Algorithms and Med-Systems vol. 8, pp.195-206
• [5] (www.statsoft.com, 2011). Downloaded 11 20, 2011
• [6] Tuffery, S. (2011). Data Mining and Statistics for Decision Making. Wiley.
• [7] Du, H. (2010). Data Mining Techniques and Applications. An introduction. Cengage Learning EMEA.