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More specifically, we calculate structures and relative energies of reactant, products, intermediate and transition states involved in all the three suggested pathways (cis-trans isomerization, rearrangement, fragmentation).
We are able to calculate structures of the early folding intermediate of the model system barstar that are fully consistent with FPOP data and Φ values.
A similar computational methodology was used in Majumdar et al. [72] to calculate structures of the UO2 CO3) complex, but these results predicted U-O bond lengths of ≈2.3 Å. Majumdar and Balasubramanian [73] used B3LYP, MP2 and coupled cluster doubles (CCD) methods with COSMO solvation [74] to model UO2 CO3 22- (with and without Li+ and Na+) and predicted U-O(C) bonds of 2.34 Å without Li+ or Na+.
Another of Gaudí's innovations in the technical realm was the use of a scale model to calculate structures: for the church of the Colònia Güell, he built a 1 10 scale model with a height of 4 m in a shed next to the building.
The CNS program [55] with the ARIA module [56] was adopted to assign NOE peaks and to calculate structures.
The sets of validated peak lists are provided to the external programs that determine torsion angle restraints, assign NOESY peaks, calculate structures and analyze secondary structure.
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TRUNCATE from the CCP4 suite was used to calculate structure-factor amplitudes from the intensities.
Protein tertiary structure alignments were conducted by the Calculate Structure Alignment software using the jCE algorithm and default parameters [ 68].
Figure 1 Schematics of the calculated structures.
First we demonstrated that SAXS constraints work additively to NMR-derived information in calculating structures.
Both calculated structures differ geometrically in the plane plane dihedral angels, affording the three planes C14 C15 C16 C17 C18 C19, S1 C1 C2 C3 C4, and C5 C6 C7 C8 C9 C10.
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