3. Structural design

3.1 Calculation framework

Calculating the structure of a protein from NMR parameters involves determining a set of conformers of the molecule, each conformer being defined by the Cartesian coordinates of the atoms (figure 17 ). This is very different from X-ray crystallography, where only the conformations present in the crystal lattice are determined. As NMR studies molecules in solution with internal dynamics, it is normal that the end result is a set of conformations.

NMR structures are calculated using the formalism of classical...

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Structural design

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Bibliography

References

(1) - CANTOR (C.R.), SCHIMMEL (P.R.) - Biophysical Chemistry Part II. - WH Freeman et Company (1980).
(2) - THORNTON (J.M.), ORENGO (C.A.), TODD (A.E.), PEARL (F.M.) - Protein folds, functions and evolution. - J. Mol....

Websites

Databases

Protein Data Bank (PDB) https://www.rcsb.org/

BioMaguResBank (BMRB) http://www.bmrb.wisc.edu

NMR, molecular modeling

NMR Information Server http://spincore.com/nmrinfo

...

Manufacturers and suppliers

Fermenters are available to automatically control the culture of organisms for protein overexpression. These devices control pH, temperature and partial pressures of oxygen and carbon dioxide.

Fermenters

B Braun Biotech (Sartorius S.A) http://www.bbraunbiotech.com

Marked media and isotopes

...

Software

The computers used for structural calculations are mainly UNIX-based workstations. This is due to the fact that the vast majority of programs are developed in a university environment under UNIX or LINUX, with a few exceptions (particularly molecule visualization programs) which run under Windows or MacOS.