docking Archive

  • Application of a novel in silico high throughput screen to identify selective inhibitors for protein–protein interactions

    Application of a novel in silico high throughput screen to identify selective inhibitors for protein–protein interactions

    Increasing numbers of target protein structures available for computational studies makes the structure-based screening paradigm more attractive for initial hit indentification. We have developed a novel in silico screening methodology incorporating Molecular Mechanics (MM)/implicit solvent methods to evaluate binding free energies and applied this technology...

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  • Making a good water model: Molecules do conformationally change when cross from a gas to water solution

    Making a good water model: Molecules do conformationally change when cross from a gas to water solution

    Solvation energy calculation is absolutely crucial for a successful binding free energy (IC50) determination. Quantum Pharmaceuticals develops aqueous solvation models and tests them against available experimental data to validate the theoretical approaches. The graph on the left represents two types of solvation energy calculations compared...

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  • Docking validation study: PDK1-kinase (oncology)

    Docking validation study: PDK1-kinase (oncology)

    Following the classic thrombine study, we catch up with a more important target: PDK1 kinase. Pyruvate dehydrogenase kinase, isozyme 1, also known as PDK1, is a human gene.It codes for an isozyme of pyruvate dehydrogenase kinase (PDK).Pyruvate dehydrogenase (PDH) is a part of a mitochondrial...

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  • Docking validation study: classic example, thrombine

    Docking validation study: classic example, thrombine

    The Figure on the left represents a docking study of more than 200 molecules with known activity on thrombin. The protein is a well known target …. We have extracted the binding data from the BindingDB database and docked all the molecules onto a single...

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  • Protein Flexibility and False Positives detection.

    Protein Flexibility and False Positives detection.

    Standard hit identification procedure with QUANTUM software implies screening of a large compound library against a given protein target. An example of such procedure for a small set of compounds with known activities is discussed in another blog entry. Let us show first that a...

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