Sökning: "Molecular Dynamics simulations"

Visar resultat 16 - 20 av 423 avhandlingar innehållade orden Molecular Dynamics simulations.

  1. 16. Molecular simulations of G protein-coupled receptors : A journey into structure-based ligand design and receptor function

    Författare :Pierre Matricon; Jens Carlsson; Bjørn Olav Brandsdal; Uppsala universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; G Protein-Coupled Receptor; Molecular Dynamics Simulations; Free Energy Perturbation; Ligand Binding; Fragment-Based Lead Discovery; Molecular Docking Screens; Homology Modeling; GPCR Activation Mechanism; Biology with specialization in Molecular Biotechnology; Biologi med inriktning mot molekylär bioteknik;

    Sammanfattning : The superfamily of G protein-coupled receptors (GPCRs) contains a large number of important drug targets. These cell surface receptors recognize extracellular signaling molecules, which stimulates intracellular pathways that play major roles in human physiology. LÄS MER

  2. 17. Computer simulations of electronic energy transfer and a molecular dynamics study of a decapeptide

    Författare :Maria Lindberg; Umeå universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; Electronic energy transfer; Monte Carlo simulations; two-particle model; GAF-theory; anisotropic systems; fluorescence depolarization ratios; Brownian Dynamics; rotating donors; Molecular Dynamics; peptide; renin inhibitor;

    Sammanfattning : Electronic energy transfer has been investigated in pure donor systems by means of computer simulations. Calculated properties were the probability that the initially excited donor is excited at a time t after the excitation, Gs(t), the mean square displacement of the excitation and different fluorescence observables. LÄS MER

  3. 18. Simulations of ultrafast photon-matter interactions for molecular imaging with X-ray lasers

    Författare :Ibrahim Eliah Dawod; Nicusor Timneanu; Carl Caleman; Adrian P. Mancuso; Lars Schäfer; Uppsala universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; X-ray free-electron laser; molecular dynamics; radiation damage; plasma simulations; density functional theory¸ coherent diffractive imaging; protein structure; X-ray crystallography; single particle imaging;

    Sammanfattning : Biological structure determination has had new avenues of investigation opened due to the introduction of X-ray free-electron lasers (XFELs). These X-ray lasers provide an extreme amount of photons on ultrafast timescales used to probe matter, and in particular biomolecules. LÄS MER

  4. 19. Computational Modelling of Ligand Complexes with G-Protein Coupled Receptors, Ion Channels and Enzymes

    Författare :Lars Boukharta; Johan Åqvist; Christopher A. Reynolds; Uppsala universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; computer simulations; molecular dynamics; ligand binding; free energy perturbation; linear interaction energy; binding free energy; homology modelling; structure prediction; alanine scanning; site-directed mutagenesis; hERG; GPCR; neuropeptide Y; HIV-1 reverse transcriptase; integron integrase; Molecular Biotechnology; Molekylär bioteknik;

    Sammanfattning : Accurate predictions of binding free energies from computer simulations are an invaluable resource for understanding biochemical processes and drug action. The primary aim of the work described in the thesis was to predict and understand ligand binding to several proteins of major pharmaceutical importance using computational methods. LÄS MER

  5. 20. Advances in Ligand Binding Predictions using Molecular Dynamics Simulations

    Författare :Henrik Keränen; Johan Åqvist; Jordi Villà i Freixa; Uppsala universitet; []
    Nyckelord :NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; free-energy perturbation; molecular dynamics; ligand binding; free-energy perturbation; linear interaction energy; binding free-energy; homology modeling; virtual screening; alanine scanning; amino acid mutagenesis; hERG; GPCR; adenosine receptor; serotonin receptor; BRICHOS; cruzain;

    Sammanfattning : Biochemical processes all involve associations and dissociations of chemical entities. Understanding these is of substantial importance for many modern pharmaceutical applications. In this thesis, longstanding problems with regard to ligand binding are treated with computational methods, applied to proteins of key pharmaceutical importance. LÄS MER