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Massey SE. ScanMoment: a web server for combinatorial analysis of basic residues in nucleic acid binding sites. Bioinformation. 2009;3(7):293-5doi: 10.6026/97320630003293.
Massey, S. E. (2009). ScanMoment: a web server for combinatorial analysis of basic residues in nucleic acid binding sites. Bioinformation, 3(7), 293-5. https://doi.org/10.6026/97320630003293
Massey, Steven E. "ScanMoment: a web server for combinatorial analysis of basic residues in nucleic acid binding sites." Bioinformation vol. 3,7 (2009): 293-5. doi: https://doi.org/10.6026/97320630003293
Massey SE. ScanMoment: a web server for combinatorial analysis of basic residues in nucleic acid binding sites. Bioinformation. 2009;3(7):293-5. doi: 10.6026/97320630003293. Epub 2009 Feb 27. PMID: 19293994; PMCID: PMC2655046.
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Bioinformation. 2009;3(7):293-5. doi: 10.6026/97320630003293. Epub 2009 Feb 27.

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

Bioinformation

Steven E Massey

Affiliations

  1. Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan, Puerto Rico 00931. [email protected]

PMID: 19293994 PMCID: PMC2655046 DOI: 10.6026/97320630003293

Abstract

UNLABELLED: 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.

AVAILABILITY: www.scanmoment.org.

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

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