Search for dissertations about: "Johan Åqvist"

Showing result 1 - 5 of 18 swedish dissertations containing the words Johan Åqvist.

  2. 1. From Structure to Function with Binding Free Energy Calculations for Codon Reading, Riboswitches and Lectins

    Author : Johan Sund; Åqvist Johan; Javier Luque; Uppsala universitet; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; binding free energy; ribosome; codon reading; release factor; mitochondrial translation; purine riboswitch; lectin; molecular dynamics; free energy perturbation; Biology with specialization in Structural Biology; Biologi med inriktning mot strukturbiologi;

    Abstract : Molecular association is part of many important processes in living cells. Computational methods for calculating binding free energies allows for a quantitative examination of biomolecular structures and hypotheses drawn from biochemical experiments. READ MORE

  4. 2. Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes

    Author : Martin Almlöf; Johan Åqvist; Chris Oostenbrink; Uppsala universitet; []
    Keywords : Theoretical chemistry; computer simulations; molecular dynamics; linear interaction energy; binding free energy; linear response; protein-protein interactions; structure-based design; point mutations; hot spots; solvation free energy; Teoretisk kemi;

    Abstract : The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented. READ MORE

  5. 3. Computational Analysis of Molecular Recognition Involving the Ribosome and a Voltage Gated K+ Channel

    Author : Martin Andér; Johan Åqvist; Lennart Nilsson; Uppsala universitet; []
    Keywords : NATURVETENSKAP; NATURAL SCIENCES; NATURVETENSKAP; NATURAL SCIENCES; computer simulations; molecular dynamics; ligand binding; binding free energy; linear interaction energy; codon recognition; translation termination; release factor; voltage gated potassium ion channel; Kv1.5; Structural biology; Strukturbiologi; Biochemistry; Biokemi; Biokemi; Biochemistry;

    Abstract : Over the last few decades, computer simulation techniques have been established as an essential tool for understanding biochemical processes. This thesis deals mainly with the application of free energy calculations to ribosomal complexes and a cardiac ion channel. READ MORE

  6. 4. Molecular Simulation of Enzyme Catalysis and Inhibition

    Author : Sinisa Bjelic; Johan Åqvist; Adrian J. Mulholland; Uppsala universitet; []
    Keywords : Theoretical chemistry; enzyme catalysis; enzyme inhibition; computer simulations; molecular dynamics; empirical valence bond method; structure-based inhibitor design; Teoretisk kemi;

    Abstract : The reaction mechanisms for the hemoglobin degrading enzymes in the Plasmodium falciparum malaria parasite, plasmepsin II (Plm II) and histo-aspartic protease (HAP), have been analyzed by molecular simulations. The reaction free energy profiles, calculated by the empirical valence bond (EVB) method in combination with molecular dynamics (MD) and free energy perturbation (FEP) simulations are in good agreement with experimental data. READ MORE

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

    Author : Lars Boukharta; Johan Åqvist; Christopher A. Reynolds; Uppsala universitet; []
    Keywords : 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;

    Abstract : 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. READ MORE