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Title

 

Ligation site in proteins recognized in silico

 

Authors

 

Michal Brylinski1,2, Leszek Konieczny3, Irena Roterman1,4,*

 

Affiliation

 

1Department of Bioinformatics and Telemedicine, Collegium Medicum Jagiellonian University, Kopernika 17, 31-501 Krakow, Poland; 2Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland; 3Institute of Medical Biochemistry, Collegium Medicum Jagiellonian University, Kopernika 7, 31 034 Krakow, Poland; 4Faculty of Physics, Jagiellonian University, Reymonta 4, 30-060 Krakow, Poland

 

E-mail*

 

myroterm@cyf-kr.edu.pl; * Corresponding author

 

Article Type

 

Current Trends

 

Date

 

received March 27, 2006; accepted April 5, 2006; published online April 11, 2006

 

Abstract

 

Recognition of a ligation site in a protein molecule is important for identifying its biological activity. The model for in silico recognition of ligation sites in proteins is presented. The idealized hydrophobic core stabilizing protein structure is represented by a three-dimensional Gaussian function. The experimentally observed distribution of hydrophobicity compared with the theoretical distribution reveals differences. The area of high differences indicates the ligation site.

 

Availability

 

http://bioinformatics.cm-uj.krakow.pl/activesite

 

Keywords

 

 

hydrophobicity; active site; function recognition; protein structure

 

Citation

 

Brylinski et al., Bioinformation 1(4): 127-129 (2006)

 

Edited by

 

P. Kangueane

 

ISSN

 

0973-2063

 

Publisher

 

Biomedical Informatics

 

License

 

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.