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Bioinformation. 2009; 3(7): 293–295.
Published online 2009 February 27.
PMCID: PMC2655046

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

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 hus likely to possess a BFAH motif. The user may vary the periodicity from that of an alpha‐helix (100°), 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.

Availability

www.scanmoment.org.

Keywords: basic moment, Fourier transformation, periodicity, alpha helix, Aspartyl‐tRNA synthetase

Articles from Bioinformation are provided here courtesy of Biomedical Informatics Publishing Group