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Molecular design and synthesis of drugs should be based on high resolution structures and analysis of specific compounds and host molecules; however, it is necessary to obtain crystals for X-ray structural analysis.
Similar to eSynth, FOG employs a construction algorithm using molecular fragments to generate synthetically tractable molecules, however, it grows molecules using a Markov Chain according to statistics on the frequency of specific connections in the database of chemicals.
This model is compatible with our conclusion that multiple unscrambling pathways may produce functional macronuclear molecules; however, it does not predict the distinct stages that we see during gene unscrambling.
GAFF's accuracy is impressive when applied to small molecules; however, it is a fixed-charge, nonpolarizable model, so one may therefore question to what extent its quality may degrade when applied to larger systems.
Computer simulations suggested that the widely used concept of half-life underestimated the averaged life-span of mRNA molecules; however, it is still a major factor that determines the life-span of different steps in the degradation pathway.
Attaching the targeting motif to the triazole would be feasible and result in relatively small molecules; however, it would need to be attached directly to the triazole, rather than through a linker (compare 8 and 9 with 12).
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Applying valence bond theory to ferrocene by considering an Fe2+ centre and two cyclopentadienide anions (C5H5−), which are known to be aromatic according to Hückel's rule and hence highly stable, allowed correct prediction of the geometry of the molecule; however, it was only once molecular orbital theory was successfully applied that the reasons for ferrocene's remarkable stability became clear.
Many studies have been done to increase the specificity of the measurement of αFP for the diagnosis of HCC depending on its binding capacity to different molecules; however its use is expensive and it is not widely available[ 2, 42].
Molecule B (Fig. 3) was similar in structure but slightly smaller in size than molecule A. However, it had only one stable pose when docked to LYN, compared to a dozen stable poses when docked to Plk1.
Many intracellular systems have been reconstructed by assembling molecules, however the mechanism to synthesize its own constituents by self-sufficient energy has to the best of our knowledge not been developed.
Heparin is also a small molecule (8 kDa); however, it did not seem to leak into the circulation in our experiments.
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Justyna Jupowicz-Kozak
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