This SOP describes the preparation of pteridine ligand 3D structures from SMILES or other input formats with the LigPrep routine as embedded in Schrödinger Maestro for usage in docking runs and in silico ADME-Tox property prediction.
This SOP describes the docking receptor preparation of PTR1 and DHFR receptor PDB files, performed with the Maestro Protein PrepWizard and the Glide grid generation routine. The optional identification and integration of conserved structural water molecules with the WatCH tool is also covered.
This SOP describes the docking of pteridine libraries into PTR1 or DHFR target receptors, using Glide and Prime in Schrödinger Maestro as part of the Induced Fit workflow to allow for receptor side chain reorganization upon ligand binding.
This file contains the R-script to analyse single nuclei and single cell data of Bl6 and Fzt:DU mice previously processed with cellranger. The analyses utilizes the Seurat and harmony package to integrate three datasets before subsequent downstream analysis characterizing proliferative cardiomyocytes.
Protocol for the extraction of biomolecules (DNA,RNA,protein,metabolties) from the same sample. Originally intended for lipid accumulating organisms (LAO) from wastewater treatment plant samples.
So far succesfully used for pelleted cells from planktonic cultures.
Metabolomics perturbation sample preparation and description of how the exact details of the perturbations.
-Amino acid starvation
-Oxidative stress via H2O2
-Glycerol addition to the medium
We have adapted the definitions of terms in [ISA best practice] and [programmes and projects]:
Programme = Overarching research theme (The Digital Salmon)
Project = Research grant (DigiSal, GenoSysFat)
Investigation = a particular biological process, phenomenon or thing
(typically corresponds to [plans for] one or more closely related papers)
Study = experiment whose design reflects a specific biological research question
Assay = standardized measurement or diagnostic experiment using a
Oxygen gradients were developed as a quick and easy way to simultaneously adapt (recombinant) strains to decreasing levels of oxygen and monitor their progress over multiple days. This SOP can be used for o/n checks or for adaptation experiments spanning over multiple days. For the latter, a time-lapse camera setup is recommended.
This SOP can also be applied to check the oxygen requirements of unknown strains.