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QUANTUM SOFTWARE DESRIPTION

Quantum is a suite of drug discovery software designed to enhance stages of drug discovery workflows, such as target identification, drug hit identification, lead identification and lead optimization. Quantum was developed with a new paradigm in molecular modeling – applying quantum and molecular physics instead of statistical scoring-function-like and QSAR-like methods.

Key Quantum Benefits:

  • Outstanding precision of molecular modeling and calculations
  • Very effective in creating revolutionary new medicine and the ability to discover novel classes of inhibitors
  • Really easy-to-use interface due to homology of applications and doesn’t require intensive training
  • Runs on Linux/Windows
  • Multiprocessors’ version
  • Flexible licensing options
Quantum consists of the following modules:
  1. The IC50 of a protein-ligand complex:

    2. 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
    For more information see this section in the User Manual.

  2. Ligand docking:

    3. 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
    For more information see this section in the User Manual.

  3. Library screening:

    4. 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
    For more information see this section in the User Manual.

  4. The IC50 for a protein-protein complex:

    5. 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
    For more information see this section in the User Manual.

  5. Large-scale protein movements:

    6. 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
    For more information see this section in the User Manual.

  6. Lead Selectivity test (ProteinSpectrumScreen):

    7. 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
    For more information see this section in the User Manual.

  7. Mutagenesis:

    8. 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
    For more information see this section in the User Manual.

  8. Rational drug design:

    9. 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
    For more information see this section in the User Manual.

  9. Solubility:

    10. 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
    For more information see this section in the User Manual.

  10. Model build:

    11. 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
    For more information see this section in the User Manual.

  11. Superimpose:

    12. This procedure provides the best fit for two molecules.
    Application Area: computational chemistry
    For more information see this section in the User Manual.

  12. Visualization tools:

    13. A molecular visualization program for displaying, animating, constructing and analyzing large bio-molecular systems using 3-D graphics.
    Application Area: computational chemistry and modeling
    For more information see this section in the User Manual.

  13. Protein-ligand complex library:

    14. 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
    For more information please follow this link.

  14. Small-molecule library:

    15. 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


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    _____________________________________________________ Related fields: Computer Aided Drug Design Insilico Measuring Inhibition constant tool Affinity estimation Binding Prediction IC50 Value Determenation Measurement Modelling Toxic effects Adverse and unexpected therapeutic activity ADMET Absorption Distribution Metabolism Excretion estimate Toxicity CADD CAMM Toxicology Ki Free Binding Energy Research Discover Inhibitor Agonist Antagonist calculated concentration of an inhibitor pKd Values assessment post-QSAR technology IT Prediction of Inhibitory Drug Interactions ki kI
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