Contacts for nitrogen, singly bonded to a planar structure (f29) — e.g. in carbamoyl group.

<p>showing distance dependence for target class <b>C14</b> (carbonyl oxygen). The scatter plot contains all <b>C14</b> target atoms in the training data and the densities show which directions are emphasized at distances 2.7, 2.98 and 3.26 Å.</p

Classification of contact atoms, or targets.

<p>The target classification was adopted from the previous work of Rantanen et al. (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049216#s1" target="_blank">Introduction</a>) while some classes were excluded. As in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049216#pone-0049216-t002" target="_blank">Table 2</a>, the classes are not renumbered for the consistency of notation.</p

Criteria for selecting structures from PDB.

<p>Criteria for selecting structures from PDB.</p

A ROC curve illustrating the functionality of the probabilistic model.

<p>The 12 threshold probabilities separating ligands from decoys that were used for calculating the characteristics are 0.05, 0.1, …, 0.3, 0.4, 0.5, 0.65, 0.75, 0.8 and 0.9.</p

The volumes used for calculations in Examples 1,3 and 4.

<p>Here would be located in the center of the volume, both radially and with respect to the solid angle. The center of the volume of Example 2 (not shown explicitly) is located on the axis defined by the vector connecting Atom1 to Main-atom, i.e. on the positive x-axis in this figure.</p

R-Norepinephrine (PDB ligand identifier: LT4) with amino acid residues that contain target atoms having highest probability density values in the model.

<p>In the figures on the right, the double contacts are created by a degeneracy that follows from the way the fragments are defined. Namely, the third atom (Atom2, see Section Data collection and processing) of a fragment in a molecule can frequently be chosen from more than one possible atom and each choice creates its own probability density, including a maximum. These densities are connected through a rotation around the covalent bond between the Main-atom and Atom1.</p

Prior probabilities for fragment classes used in this study.

<p>Classes C10 to C15.</p

Properties of the second set of decoys in Example 6.

<p>Index values represent an ordering of the molecules in this study.</p

Probability density modeling the target cloud of <b>Figure 1</b>.

<p>It is depicted in the same reference frame with the density. They can be interpreted as overlayed such that elevations in the density correspond to dense areas in the cloud of data points. The main direction of the fragment, as described in the caption of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049216#pone-0049216-g001" target="_blank">Figure 1</a>, is defined by in the reference frame of the model, but corresponds in this figure to , where is the polar angle and is the azimuthal angle.</p

Model based probabilities calculated from the reference poin 1 centerd volume.

<p>The probability masses have been obtained with a model that was trained using a dataset from which the additives were excluded.</p