Search for dissertations about: "protein–ligand binding"

Showing result 1 - 5 of 7 swedish dissertations containing the words protein–ligand binding.

  2. 1. QM/MM free-energy perturbation and other methods to estimate ligand-binding affinities

    Author : Martin Olsson; Beräkningskemi; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; Computer-aided drug design; protein–ligand binding; molecular dynamics; free-energy perturbation; QM MM; convergence;

    Abstract : Experimental drug discovery is very time-consuming, risky and comes at a huge cost, typically several billion USD per drug. Even though decades of experimental drug discovery have provided cures of many diseases, there are still diseases for which there is no effective drug available. READ MORE

  4. 2. A first-principles approach to protein–ligand interaction

    Author : Pär Söderhjelm; Beräkningskemi; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; solvation; exchange repulsion; polarizable force fields; polarization; molecular mechanics; quantum chemistry; intermolecular interactions; protein–ligand interaction;

    Abstract : It is still impossible to make an accurate, purely theoretical prediction of the free energy of a ligand binding to a protein in aqueous environment. The two main problems are the immense number of nuclear configurations contributing to the binding free energy and the impossibility to apply accurate quantum-chemical methods to such a large system, even for a single configuration. READ MORE

  5. 3. Theoretical studies of protein-ligand binding

    Author : Majda Misini Ignjatovic; Beräkningskemi; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; Protein-ligand binding; MD; GIST; GCMC; FEP; Solvation; Entropy; Water; QM MM-FEP; Protein-ligand binding; MD; GIST; GCMC; FEP; Solvation; Entropy; Water; QM MM-FEP;

    Abstract : Understanding how drugs work is of great importance, since it can facilitate drug discovery, both time- and costwise. At the same time, it is important to have methods that can help predict how well does a potential drug molecule bind to its target. Computational methods can in many ways contribute to drug design process. READ MORE

  6. 4. Free-energy studies of ligand-binding affinities

    Author : Vilhelm Ekberg; Beräkningskemi; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; free energy perturbation; drug design; ligand-binding affinity; entropy; molecular mechanics; molecular dynamics;

    Abstract : In drug discovery, it is of utmost importance to accurately calculate the free energies of binding ligands to various protein targets, such as enzymes and receptors. We have assessed and used computational tools for this aim, most of them based on molecular dynamics (MD) simulations. READ MORE

  7. 5. Molecular recognition and dynamics in proteins studied by NMR

    Author : Johan Wallerstein; Biofysikalisk kemi; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; Chemical exchange; Conformational entropy; Entropy; Galectin-3; Isothermal Titration Calorimetry; ITC; Model-free formalism; Molecular recognition; Nuclear Magnetic Resonance; NMR; PGB1; Protein dynamics; Protein–ligand interactions; Proton-transfer reactions; Spin relaxation; Viscosity; Chemical exchange; Conformational entropy; Entropy; Galectin-3; Isothermal Titration Calorimetry; ITC; Model-free formalism; Molecular recognition; Nuclear Magnetic Resonance; NMR; PGB1; Protein dynamics; Protein–ligand interactions; Proton-transfer reactions; Spin relaxation; Viscosity;

    Abstract : Knowledge of dynamics in protein is very important in the description of protein function and molecular recognition. The thesis investigates protein dynamics on time-scales from milli- to sub-nanosecond, with focus on the latter, using NMR spin relaxation experiments on two proteins, the 138-residue carbohydrate recognition domain of galectin-3 (Gal3C) and the 56-residue B1 domain of bacterial protein G (PGB1). READ MORE