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Nucleic Acids Research 2004 32(Web Server Issue):W104-W107; doi:10.1093/nar/gkh363
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins

Shandar Ahmad* and Akinori Sarai

Department of Biochemical Science and Engineering, Kyushu Institute of Technology, Iizuka 820 8502, Fukuoka-ken, Japan

* To whom correspondence should be addressed. Tel: +81 948 29 7841; Fax: +81 948 29 27841; Email: shandar{at}bse.kyutech.ac.jp

Received February 13, 2001; Revised and Accepted March 4, 2004

We have developed a simple but powerful method and web server to quickly locate charged and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html). For the charged clusters, each atom in the protein is first assigned a charge according to a standard force field. Then a box is created with dimensions corresponding to the range of atomic coordinates. This box is then divided into cubic grids of selected size, which now have one or more charged atoms in them. This leaves each grid with a certain amount of charge. Cubic grids with more than a cutoff charge are then clustered using a hierarchical clustering method based on Euclidean distance. A tree diagram made from the resulting clusters indicates the distribution of charged and hydrophobic regions of the protein. Hydrophobic clusters are developed by grouping the positions of C{alpha} atoms of such residues. We propose that such a tree representation will be helpful in detecting protein–protein interfaces, structure similarity and motif detection.

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