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Images were acquired automatically with a spinning disk confocal microscope, and the individually labelled DNA molecules were manually measured with ImageJ.
Molecules were manually selected utilizing expert knowledge so they can be assigned to six clusters representing the original six combinatorial libraries the compounds were synthesized in.
A subset of 298 randomly chosen molecules were manually assigned in order to perform the evaluation by direct comparison of predicted and observed chemical shifts and compare the results obtained with those produced by our method.
The water molecules were manually deleted prior to submitting the PDB files to the GETAREA web service (http://curie.utmb.edu/getarea.html).html
Water molecules were manually placed on the basis of typical criteria: electron density of ≥3ρrms in Fo – Fc maps and ≥0.8ρrms in 2 Fo – Fc maps and a reasonable potential H-bond partner.
All molecules were manually linked to their related genes, whereas heterodimer protein complexes in the list of candidates (e.g., PPARA RXRA) were switched into two genes encoding the corresponding partners (e.g., PPARA and RXRA).
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Detailed methods outlining criteria by which molecules are manually rejected for testing even though they are high-ranking in the virtual screen.
In the next step, the C or 5 mC bismonophosphate molecule was manually docked to each of the starting structures.
The protonation state of each molecule was manually set according to the pH value at which the measurement was performed.
The presence of each water molecule was manually validated.
To test this, several cell aggregates in OSKMT plus small molecule group were manually picked 4 weeks after transfection and subjected to RT-PCR analysis.
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