In preparation section, Prepare Protein module in Discovery Studio 2.5 (DS 2.5) was employed to protonate the X-ray crystallography structure of TRAF6 protein with Chemistry at HARvard Macromolecular Mechanics (CHARMM) force field [ 39] and remove crystal water.
Tissues were prepared for histopathology (paraffin preparation, sectioning, and hematoxylin and eosin staining) and analyzed by subsequent microscopic evaluation by IDEXX Veterinary Services (West Sacramento, CA, USA).
Samples were prepared as described in 'sample preparation' section.
In order to verify the advantage of suspension digestion, dough was prepared according to the 'Sample preparation' section.
In preparation section, the PKM2 proteins were prepared by pdb2gmx protocol of Gromacs to provide topology and parameters with CHARMM27 force field, and each ligand was prepared by SwissParam program [ 28] to provide topology and parameters with CHARMM.
See the preparation section for more information on preparing aquarium water.
Only use water carefully selected or prepared with the instructions in the preparation section.
Biotin-labeled dsDNA (1.5 × 10-8 nmol), prepared as described in the DNA probe preparation section, was added to an appropriate concentration of nuclear extract.
In preparation section, the IDH2 R140Q mutant proteins were prepared by pdb2gmx protocol of Gromacs to provide topology and parameters with charmm27 force field, and each ligand was prepared by SwissParam program [ 51].
The newly prepared inoculum for the algal disks (refer to the ' Inoculum preparation' section) was collected by centrifugation at 5,000 × g for 30 s (Allegra X-22R, Beckman Coulter, Brea, CA, USA).
