ScanMoment: a web server for combinatorial analysis of basic residues in nucleic acid binding sites.
ScanMoment is a webserver designed to identify the presence of the basic faced alpha-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 alpha-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 degrees ), to those of other secondary structures such as beta sheets and 3(10) 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.


BACKGROUND
www.scanmoment.org.
Massey
Steven E
SE
Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan, Puerto Rico 00931. stevenemassey@gmail.com