Sentence examples for based on the atom from inspiring English sources

To assess the surface exposure of the amino acids in the protein structure, we used the GETAREA 1.1 [ 101] web-based program based on the atom coordinates of the PDB file.

By default, ACC tries to select one of these sets based on the atom types present in the uploaded molecules.

The proposed algorithm in the SMSD checks if two molecules are identical or dissimilar based on the atom count and bond count before performing the MCS search.

The diagram of ∆x based on the atom index in Y direction (j) is drawn in Figs. 4, and 5, for the two dimer numbers, 29 and 30 (odd and even).

An InChI identifier [15] is a canonicalization based on the atom connectivity of a molecule, which in turn is derived from Cartesian coordinates for each atom using simple heuristic rules specifying a range of atom pair distances for any element combination.

The Tanimoto coefficient and the molecule names are displayed for clarity and are not shown in the PyMOL viewer Fig. 3 Example of the plugin's output after 3D screening, where two molecules are superimposed based on the atom pairs displayed on the left hand side list.

This article presents a novel descriptor based on the atom-pair property.

Optimal Assignment Kernels follow a similar concept and have been used in machine learning methods such as Support Vector Machines [23]. Figure 4 Alignment of the atoms in molecules A and B based on the atom-to-atom similarity matrix.

The final result of the optimal assignment of the atoms, based on the atom-wise similarity calculations using the differentiation with the six cases, is shown in Figure 5 on the same molecules causing topological errors using the original OAK.

An accurate quantitative structure property relationship (QSPR) model, based on the atom-type electrotopological state (E-state) indices and artificial neural network (ANN) technique, for prediction of standard net heat of combustion (ΔHco) was developed.

The 4D FAPOA entails an optimal assignment step to compute a final similarity value based on the atom-pair tree similarity matrix S. If the approach computes the similarity value between the query compound and a data set compound, the i-th row of S represents the atom-pair tree with the i-th atom of the query compound as root node.