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New parameters were incorporated in the algorithm, including chemical environment of predicted sites, overall stabilities and conformational entropy changes, the geometric deviations with pre-existing native disulfide bonds in solved high-resolution protein structures.
For any two given residues, three functions were required for evaluating the possibility of forming disulfide bond between them: 1) P Geom, the geometrical probability; 2) P RMSD, the RMSD between predicted disulfide-linked cysteines and the geometrically closest naturally occurring ones in solved structures; 3) P ΔS, the conformational entropy change induced by the engineered disulfide bond.
The most successful type of structure prediction, known as homology modeling, relies on the existence of a "template" structure with sequence similarity to the protein being modeled; structural genomics' goal is to provide sufficient representation in solved structures to model most of those that remain.
Indeed, molecular accommodation was apparent in solved structures of individual TCR bound to different pMHC complexes or when comparing free and pMHC-bound TCR [11].
These homology blocks correspond to structural elements in solved structures [ 57, 58].
The last two Ca2+ ions are not constant in solved CLDs structures.
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