Sökning: "Johan Åqvist"
Visar resultat 1 - 5 av 18 avhandlingar innehållade orden Johan Åqvist.
1. From Structure to Function with Binding Free Energy Calculations for Codon Reading, Riboswitches and Lectins
Sammanfattning : 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. LÄS MER
2. Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes
Sammanfattning : 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. LÄS MER
3. Computational Analysis of Molecular Recognition Involving the Ribosome and a Voltage Gated K+ Channel
Sammanfattning : 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. LÄS MER
4. Molecular Simulation of Enzyme Catalysis and Inhibition
Sammanfattning : 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. LÄS MER
5. Computational Modelling of Ligand Complexes with G-Protein Coupled Receptors, Ion Channels and Enzymes
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