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

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.

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www.scanmoment.org.

SUBMITTER: Massey SE

PROVIDER: S-EPMC2655046 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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

Massey Steven E SE

Bioinformation 20090227 7

<h4>Unlabelled</h4>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 perio ...[more]

PMID: 19293994

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