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The justification for this penalty is that adjacent residues that are highly interactive should be part of the same interaction core and therefore should not be split.
The residues that form the interaction core between the coiled α-helices are the "a" and the "d".
The glycan array analysis was conducted by the Protein-Carbohydrate Interaction Core H of The Consortium for Functional Glycomics.
According to van Raaij and co-authors, at positions "c", "e", and "k" there are hydrophobic residues forming the hydrophobic interaction core, whereas pairs (f, c), (h, c), (j, a), (i, e) are involved in an hydrogen bonding network.
We also verified that the IRACC measure of the interaction core alignment generated by CMAPi on SCOPPI correlates well with the more standard RMSD measure (Fig. 5a).
The Consortium for Functional Glycomics (CFG) group also has a Protein-Carbohydrate Interaction Core facility which applies two different methodologies for protein analysis and glycan recognition.
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This usually induces a large work overhead when specialists from the two domains try to connect their applicative studies, especially when developing augmented reality systems that feature complex interaction cores.
Increasing doses of d-amphetamine also increased perseverative responding (Dose: F2,44 = 9.51, P < 0.001), with a trend towards a Dose × Lesion interaction (core-lesioned rats made more perseverative responses after the highest dose of amphetamine) but this interaction did not reach significance (F4,44 = 2.3, P = 0.074).
CMAPi has accuracy almost identical to LTHREADER, while not requiring predefined interaction cores (Table 1).
A similar definition is applied to define interaction cores in { R} sequences.
Thus the interaction cores consist of contiguous stretches of aligned residues within the { L} and { R} protein sequences.
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