Dictionary

Active ligand - ligand interacting with a definite protein with a free energy less than -9 kcal/mol.

Coefficient of correlation R² - the number characterizing the correlation between two sets of numbers. In the case of absence of correlation R² = 0, in the case of total correlation R² = 1.

Docking - methods of predicting the native pose of the ligand in the protein binding site.

Docking functions SD - scoring functions used for docking - for defining the native pose of the ligand in the protein binding site. The minimum value of the score in docking must correspond to the native pose of the ligand in the binding site.

Free energy of interaction G - quantity determining the force of ligand-protein binding.

Ligand - molecule of an organic chemical substance with a molecular weight less than 500 a.u.

Ligand-protein binding - interaction of a ligand molecule with a protein molecule, leading to the formation of a stable molecular complex consisting of said molecules.

Native pose of ligand in protein binding site - the most probable pose of the ligand in the protein binding site.

Protein binding site - definite place in a protein molecule, wherein ligand molecules become bound to the protein molecule.

Quality of docking D - ratio of successful dockings to the total number of dockings.

Score S - the number defined by the structure of the ligand, by the structure of the binding site and depending on the pose of the ligand in the binding site.

Scoring - methods of predicting the free energy of the ligand-protein interaction.

Scoring functions - set of methods, functions and parameters with the help of which score S is calculated.

Scoring functions for scoring SS - scoring functions used for defining the free energy of the ligand-protein interaction. The value of the score calculated in the native pose must be proportional to the free energy of the ligand-protein binding.

Successful docking - docking, as a result of which the root-mean-square deviation between heavy atoms (RMSD) for the best-score pose of the ligand obtained as a result of docking and the native pose is less than 2 angstrems.