Sentence examples for alignments of compounds from inspiring English sources
Most of current 3D-QSAR algorithms use alignments of compounds at the training set based on reference active ligands in the first step of the construction of the pharamacophore modeling.
Users can enable 3D alignment of compounds, which is appropriate when the dataset contains structurally similar compounds.
It involves creation of 3-dimensional structure (mmff94 force field), feature extraction (Chemical Development Kit (CDK) and hashed finger prints), clustering (k-means cascade method), embedding in 3-D space (or Dimensionality reduction) and alignment of compounds using maximum common subgraph (MCS).
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.
Due to the fact that the results – and consequently our interpretations – of the docking procedure might be erroneous we performed an additional flexible alignment of compounds 1, 4, 5, and 6, and calculated a consensus pharmacophore model (Figure 3B).
Hits are determined by a hybrid similarity score cut-off and alignment poses of compounds will be generated by enumerating all potential pharmacophore feature triplets matches.
Five-point common pharmacophore hypotheses (AAAAR.38) were selected for alignment of all compounds.
It has diverse applications ranging from lead prediction to automated reaction mapping and visual alignment of similar compounds.
The final wizard step allows to configure the alignment of the compounds inside a cluster according to a common substructure (see Figure 9).
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.
Results in Table 2 showed that all the active compounds were able to satisfy the pharmacophoric features of the generated model with RMSD values ranging from 0.3907 to 0.6571 Å along with their most suitable alignment of each compound over query.
