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The tables in the Hit Analysis module contain a number of different scores which can help you identify hits, distinguish between competitive and non-competitive hits or suggest peaks that need to be inspected and checked manually.
The Peak Binding Scores are provided in the Peak Binding Scores Table (see our Hit Analysis Tables page for more information on this table). The way in which the Peak Binding Scores are calculated is determined by the selections made in the Settings panel Calculation tab. The Mode specifies whether the peak height, line width or volume are used for the calculation. Note that peaks have to have been fitted (e.g. with RG) to determine the line width, and volume estimation also has to be done explicitly (e.g. with EV). The Engine specifies the equation used to calculate the Binding Score. Hovering over each option in the Calculation panel, will show you the equations used:
Simple Ratio
T / C
where
T : +Target. Ligand signal in the presence of the target.
C : -Target. Ligand signal in the absence of the target (Control).
A lower value indicates a greater value change, e.g. a larger intensity drop. A value of 1 indicates no changes between +Target and -Target signals. Values above 1 might suggest scaling issues.
Relative Change
(C-T) / C
where
T : +Target. Ligand signal in the presence of the target.
C : -Target. Ligand signal in the absence of the target (Control).
A lower value indicates a greater value change, e.g. a larger intensity drop.
Absolute Relative Change
||C|-|T|| / |C|
where
T : +Target. Ligand signal in the presence of the target.
C : -Target. Ligand signal in the absence of the target (Control).
A lower value indicates a greater value change, e.g. a larger intensity drop.
AbsoluteRelativeDifference
|C-T| / (|T+C| / 2)
where
T : +Target. Ligand signal in the presence of the target.
C : -Target. Ligand signal in the absence of the target (Control).
A lower value indicates a greater value change, e.g. a larger intensity drop. A value of zero indicates no changes.
STD efficiency
|off−on| / |off|
where
off : Ligand signal from the Off resonance spectrum.
on : Ligand signal from the On resonance spectrum.
A lower value indicates a lower efficiency.
WLOGSY Factor
|T – C| / |C|
where
T : +Target. Ligand signal in the presence of the target.
C : -Target. Ligand signal in the absence of the target (Control).
A lower factor might indicate a solvent-exposed atom, a higher factor might indicate a buried atom.
User defined equation
Here you can define your own equation using the variables V1 and V2.
V1 : +Target. Ligand signal in the presence of the target. Or for STD experiments: Ligand signal from the Off resonance spectrum.
V2 : -Target. Ligand signal in the absence of the target (Control). Or for STD experiments: Ligand signal from the On resonance spectrum.
Note that absolute values need to be specified as abs(V1) rather than |V1|.
The Peak Displacement Scores are provided in the Peak Binding Scores Table (see our Hit Analysis Tables page for more information on this table). The way in which the Peak Displacement Scores are calculated is determined by the selections made in the Settings panel Calculation tab. As with the Binding Score, the Mode specifies whether the peak height, line width or volume are used for the calculation. Note that peaks have to have been fitted (e.g. with RG) to determine the line width, and volume estimation also has to be done explicitly (e.g. with EV). The Displacement Engine specifies the equation used to calculate the Binding Score. Hovering over each option in the Calculation panel, will show you the equations used:
Displacement Fraction
[(D/C) - (T/C)] / 1-(T/C)
where
T : +Target. Ligand signal in the presence of the target.
C : -Target. Ligand signal in the absence of the target (Control).
D : +Target+Displacer. Ligand signal in the presence of the target and displacer (Displacer).
A lower factor might indicate a solvent-exposed atom, a higher factor might indicate a buried atom.
User defined equation
Here you can define your own equation using the variables V1, V2 and V3.
V1 : +Target. Ligand signal in the presence of the target.
V2 : -Target. Ligand signal in the absence of the target (Control).
V3 : +Target+Displacer. Ligand signal in the presence of the target and displacer (Displacer).
Note that absolute values need to be specified as abs(V1) rather than |V1|.
In the Substance and Samples tables the Binding and Displacement Scores are aggregated for each Substance or Sample from the constituent Peak Binding/Displacement Scores. The way in which this is done is specified by the TotalScore in the Settings Calculation panel. It can be set to minimum, maximum, standard deviation, mean or sum. You can also select to scale the scores from 0-1 if you wish.
The Signal/Noise ratio observed for the peaks in the Control spectra are provided in the Peak Binding Scores Table. In the Substances Tables these are aggregated across all peaks in the Substance according to the selection made in the Settings Calculation panel. Options for the Relative SNR are minimum, maximum, mean, standard deviation or median.
Peak Matching Scores are provided in the Peak Binding Scores Table. They are calculated when the peak matching is conducted automatically, and represent a quality score for how reliable the matching is. The Peak Matching Scores run from 0-5 with 5 representing a highly reliable match and 0 representing an unreliable match. We recommend that you manually inspect and check matches with a Peak Matching Score of 3 or less.
An aggregated Substance/Sample Matching Score is provided in the Substance and Samples Tables. In the Settings Matching tab you can select how this is done by setting Total Score to minimum, maximum or mean.