The phrase "alignment of the compounds" is correct and usable in written English.
It can be used in scientific or technical contexts, particularly in chemistry or materials science, to describe how different compounds are arranged or organized in relation to each other.
Example: "The alignment of the compounds in the mixture is crucial for achieving the desired chemical reaction."
Alternatives: "arrangement of the compounds" or "configuration of the compounds".
Its workflow is as follows: 1) specify a set of active compounds; 2) generate candidate pharmacophores that are solved using an algorithm via multiple flexible alignment of the active compounds; and 3) perform pharmacophore-based virtual screening.
Using spiked samples, only the correct alignment of the spiked compounds can be investigated.
When including the non-spiked samples as well, information is obtained on the alignment of the spiked compounds as well as on incorrect alignment in other areas.
The easiest way to check the quality of an alignment process is to use spiked samples of different individuals from the trial and monitor the alignment of the spiked compounds.
These marked sites give an idea about the mode of interaction of a lead molecule with Cathepsin L. As represented in Figure 5(a), an alignment of the 26 compounds from the congeneric series with that of the chosen hypothesis, DDHRR.8, supported its selection as the common pharmacophore hypothesis.
After optimization and template based alignment of these compounds, descriptors representing steric, electrostatic and hydrophobic energies at all lattice points of the grid around the molecules were computed.
The E-zyme system outputs the results of the alignment of the two compound structures and the predicted EC numbers.
The selection of the best hypothesis model was based on the total cost, predictive ability, difference in the cost from the null hypothesis and alignment of the training set compounds on to the hypothesis.
Figures 4a-c showed the alignment of the hypothesis model with compounds H5, A6, and I8 as representative examples.
The extent and the orientation of the grids surrounding the tested molecules were the same as the grid spacing was set to 2 Å. Figure 3 Alignment of compounds D1-30 withethe best 3D QSAR pharmacophore.
