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

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

Criteria for selecting structures from PDB.

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

Reference point

<p><b>.</b> Comparison of contact atom frequencies with model based probabilities for fragment classes <b>f2</b>, <b>f5</b>, <b>f26</b> and <b>f27</b>. Hierarchy is given by the calculated probabilities, which are represented as circles. The circles are joined with a line to illustrate tendencies among target classes. The bars represent the fractions of target atoms belonging to a particular class. Both sum to one over target classes. Also shown are standard errors for both the frequencies and the model based probabilities (joined with lines and centered around the mean values). The contact atom counts in reference data for <b>f2</b>, <b>f5</b>, <b>f26</b> and <b>f27</b> were 165, 126, 16 and 49, respectively.</p

Prior densities for model parameters.

<p>Prior densities for model parameters.</p

Hierarchies from model trained with data that excludes the additive-type ligands.

<p>These are relating to example 1. Reference points and : comparison of contact atom frequencies with model based probabilities for fragment classes <b>f2</b>, <b>f5</b>, <b>f11</b> and <b>f22</b>. Hierarchy is given by the calculated probabilities, which are represented as circles. The circles are joined with a line to illustrate tendencies among target classes. The bars represent the fractions of target atoms belonging to a particular class. Both sum to one over target classes. Also shown are standard errors for both the frequencies and the model based probabilities (joined with lines and centered around the mean values). The contact atom counts in reference data for <b>f2</b>, <b>f5</b>, <b>f11</b> and <b>f22</b> are 111, 67, 1 and 6, respectively.</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

Fragment classes used in this study.

<p>Main forms of intermolecular interaction for these fragment types are hydrogen bonding, dispersion, charged group based electrostatic and halogen bonding. The fragment classification was partly 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. To maintain consistency of the notation for easy comparison with earlier work, the classes are not renumbered.</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