- The IC50 of a protein-ligand complex:
Calculates the free binding energy and thus predicts the IC50 of a given protein-ligand complex.
Application Area: binding affinity prediction and hit/lead optimization
- Ligand docking:
This 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.
Application Area: binding affinity prediction, ligand position (in the active site) prediction and hit/lead optimization
- Library screening:
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.
Application Area: hit/lead identification and hit/lead optimization
- The IC50 for a protein-protein complex:
Calculates the free binding energy and predicts the IC50 of any protein-protein complex with known coordinates.
Application Area: binding affinity prediction for a protein-protein complex
- 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.
Application Area: macromolecular modeling, target identification and crystallography
- Lead Selectivity test (ProteinSpectrumScreen):
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 ADME/TOX-associated proteins.
Application Area: lead optimization – ADME/TOX prediction to 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.
Application Area: mutagenesis research, macromolecular modeling and target identification
- Rational drug design:
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.
Application Area: hit identification
- Solubility:
Calculates the solvation energy and solubility for a molecule or a library of molecules in a number of solvents (water and DMSO).
Application Area: broad application, e.g., preparation for in-vitro experiments
- Model build:
For a given molecule/atoms, this procedure adds hydrogen atoms, sets the protonation state, sets the charges and does geometrical optimization.
Application Area: broad application, e.g., computational chemistry
- Superimpose:
This procedure provides the best fit for two molecules.
Application Area: computational chemistry
- Visualization tools:
A molecular visualization program for displaying, animating, constructing and analyzing large bio-molecular systems using 3-D graphics.
Application Area: computational chemistry and modeling
- Protein-ligand complex library:
Provides information on the IC50 for about 300 protein-ligand complexes (publicly available in the PDB) and provides their 3D structures, which are ready-to-use to calculate the IC50 by using Quantum.
Application Area: a test set for Quantum
- Small-molecule library:
Provides a link on a web page to the Quantum Pharmaceuticals corporate web site, where you can download the libraries of compounds to perform a screening.
You can download several libraries:
- a natural compounds library consisting of about 40,000 compounds;
- a synthetic compounds library consisting of about 350,000 compounds;
- a diversified synthetic compounds library consisting of about 30,000 compounds.
All structures are ready-to-use for the Library screening module – these molecules were processed by 1) adding hydrogen atoms to the complex, 2) setting the protonation state, 3) setting the charge and 3) optimizing the geometry.
Application Area: hit identification
