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Fig. 4.1 Comparison of NAD + -complexing proteins as reported by CASTp. To p : MCC; bottom :
F-measure
ranging from approximately 0.8 to a little over 0.2. Both measures (MCC and
F-measure) remained in fairly good agreement with each other - thus, we can
conclude that the results of NAD + binding site identification as returned by CASTp
are relatively trustworthy.
Of note are the quantitative differences between MCC and F-measure rankings,
which affect the ordering of each list (although they are usually restricted to close
neighbors).
MCC values reported by PocketFinder indicate relative uniformity of results,
with approximately half of the tested proteins accorded values between 0.4 and 0.5
(Fig. 4.2 ). Only two proteins scored negative values on the MCC scale. In contrast,
F-measure values are significantly more varied (a characteristic shared with other
software packages), with most results falling in the 0.1-0.3 range.
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