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Title

 

 

 

 

 

ScanMoment: a web server for combinatorial analysis of basic residues in nucleic acid binding sites

 

Authors

 

Steven E. Massey

Affiliation

 

Department of Biology, University of Puerto Rico Rio Piedras, PO Box 23360, San Juan, Puerto Rico 00931

Email

stevenemassey@gmail.com; * Corresponding authors

 

Phone

(787) 764000 x 2037

Fax

(787) 7642610

Article Type

 

Web Server

 

Date

 

received January 14, 2009; accepted January 31, 2009; published February 27, 2009

Abstract

 

ScanMoment is a webserver designed to identify the presence of the basic faced α-helix (BFAH) motif in the nucleic acid binding sites of proteins. The program calculates the 'Basic Moment', a parameter that quantitizes the distribution of basic residues on the surface of an α- helix. A sliding window is used to generate a plot displaying regions of the protein sequence that possesses a high Basic Moment and thus likely to possess a BFAH motif. The user may vary the periodicity from that of an alpha-helix (100o), to those of other secondary structures such as beta sheets and 310 helices. The program can also plot the periodicity of basic residues in a protein sequence using a Fourier transformation. The procedure has been used to characterize the presence of BFAHs in the N-terminal extensions of the eukaryotic aminoacyl-tRNA synthetases and to indicate the presence of a BFAH in the tRNA binding site of alanyl-tRNA synthetase.

 

Keywords

basic moment, Fourier transformation, periodicity, alpha helix, Aspartyl-tRNA synthetase

 

Availability

www.scanmoment.org

 

Citation

Massey, Bioinformation 3(7): 293-295 (2009)

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.