ScanMoment

ScanMoment

A methodology for the combinatorial analysis of basic residues in nucleic acid binding sites. The basic moment is a parameter that measures the periodicity of basic residues in a protein and was designed to detect the presence of basic faced alpha helices (BFAHs) in nucleic acid binding sites. For a detailed description of the basic moment and BFAHs please see the paper 'Basic Faced Alpha Helices are Widespread in the Eukaryotic Aminoacyl tRNA-synthetases'.


Calculation of the basic moment

This will calculate the basic moment for a protein sequence, using a sliding window of wither 12 or 18 residues.

Select your options:

Periodicity:
pi helix (87 degrees)
alpha helix (100 degrees)
310 helix (120 degrees)
beta sheet (160 degrees)

 Window size:
12 residues
18 residues

Enter your protein sequence:






Calculation of basic periodicity

This will calculate the periodicity of basic residues in a protein sequence segment of 18 residues

Enter your 18 amino acid sequence:




 

A Schiffer-Edmundson representation of an idealized basic faced alpha helix :

BFAH

 

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