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These FL criteria retained 84% of the molecules listed in the combined database (FragranceDB) and were used to define the fragrance like subsets PubChem.FL (1.2% of PubChem), ChEMBL.FL (0.68% of ChEMBL), ZINC.FL (0.28% of ZINC) and GDB-13.FL (6.1% of GDB-13) (Table 1).
RInChIs with no molecules listed in either layer two or layer three, or if both layers are empty, are still valid RInChIs, indicating either that these components are unknown, or else that they contain no-structure materials, about which there is more information in layer six.
Eight molecules listed in Supplementary Table S4 play important roles for differentiating stem cells into other hematopoietic lineages.
Interestingly, we found most of the molecules listed in intracellular trafficking and protein sorting mechanisms in our study given in Additional file 1: Table S1.
For further analyses of the inflammatory signaling molecules induced by TNF/CHP nanoparticles, we focused on the molecules listed in Table 1 and performed quantitative PCR analyses on 2, 6, and 26 h activated NALT cells.
To see how the estimated relative mobilities correlate to the actual relative mobilities for the small molecules listed in Table 1 and further prove that this electrophoresis based assay can be applied to these small molecules, we sulfated corresponding small molecule substrates using SULT1A1, SULT1E1, SULT2A1 and CHST4, and then separated the reactions on an 8% SDS gel.
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Drug (therapy): this is the drug (or more generally the treatment) whose effectiveness can be influenced (positively, negatively or not significantly) by the molecule listed in column "Molecule".
In the rest of this section we report the biological meaning of the factor which loadings show the clearest relation with the tissue of origin in the integrated analysis, that is F 1 for melanomas (full molecules list in Additional file 1).
Specifically, 53 out of 175 molecules in this pathway showed methylation changes of greater than 2-fold (log2) in polyps from Apcmin/+ mice; these molecules are listed in Tables 6 and 7 (30 genes with increased methylation in Table 6; 23 genes with decreased methylation in Table 7).
In building the UCD without any existing infrastructure, we had two major sources of compounds available: 1) names of molecules as listed in the literature and 2) internal working compounds, which are often referred to by their IUPAC names, common names (e.g., harmane), or CAS numbers.
The scoring function of the top 20 test-set molecules is listed in Table S2.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com