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General Information
Quantum's drug discovery tools are gathered under the Tools...
item of the Main Menu (Figure 20).
Figure 20 - Drug Discovery Tools
Tools consist of the following
items:
·
The IC50 of a protein-ligand
complex:
Calculates the free binding energy
and thus predicts the IC50 of a given protein-ligand complex.
The procedure finds the position of
a small molecule in the active site of a given protein with the minimum value
of the free binding energy and predicts the IC50 of the ligand.
Screens in silico a library of small
molecules. Finds their positions in the active site with the minimum value of
the free binding energy and predicts the IC50 values of these molecules.
· The IC50 for a
protein-protein complex:
Calculates the free binding energy
and predicts the IC50 of any protein-protein complex with known coordinates.
· Large-scale
protein movements:
This procedure provides normal mode analysis of proteins and builds
their large-scale amplitude movements. It is useful for fast evaluations of the
degree of flexibility of proteins and modeling their conformational changes.
Detects potential moderate-to-serious adverse activity, additional unexpected activity and broad relative selectivity for a library of compounds by screening them against several hundred of the ADME/Tox-Asssociated human proteins. This procedure helps prioritize the development of drug candidates.
· Mutagenesis:
Provides an interface for changing
the protein sequence at specific sites through alterations to its amino acids and
predicts changes in the bioactivity after mutations.
This tool is aimed at designing a ligand - a potential drug candidate -which
will interact specifically with a selected molecular target important in
disease progression.
· Solubility:
Calculates the solvation energy and
solubility for a molecule or a library of molecules in a number of solvents
(water and DMSO).
· Model build:
For a given molecule/atoms this
procedure adds hydrogen atoms, sets the protonations state, sets the charges
and does geometrical optimization.
· Superimpose:
·
This procedure provides the best
fit for two molecules.
·
After starting a module, a special Wizard
will appear at the bottom of the Names panel. Use the Next, Back,
and Cancel buttons of the wizard to manage the procedure.
·
All necessary instructions are
displayed on the screen. Press the Esc button to remove an instruction
from the screen.