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Fig. 4.9 Comparison of MCC and F-measure results for FMN-complexing proteins as reported by
QSiteFinder
NAD + identification results were far more varied, with some programs (particularly
CASTp and SuMo) producing correct results for proteins which could not be cor-
rectly processed by most other packages. We should also note that the phenomenon
of polypeptide chain complexation (in the form of dimers, tetramers and -
occassionally - decamers) presents significant problems for the FOD model as it
distorts each chain's hydrophobic core, producing many false positives.
Top row (left to right): 2BYC, 1B1C, 2IYG (binding site easy to identify for all
programs except FOD model)
Bottom row (left to right): 3H4O, 3CB0, 3A3B.
In most cases, accurate identification of binding sites was possible for the following
proteins:
The structural and biological characteristics of the “easy” proteins does not allow
to define the common criteria for the successful prediction. Neither monomeric/
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