Sökning: "binding free energy"

Visar resultat 1 - 5 av 119 avhandlingar innehållade orden binding free energy.

1. 1. Probing Ligand Binding Mechanisms in Insulin-Regulated Aminopeptidases : Computational analysis and free energy calculations of binding modes

   Författare :Sudarsana Reddy Vanga; Hugo Gutiérrez-de-Terán; Johan Åqvist; Efstratios Stratikos; Uppsala universitet; []
   Nyckelord :Docking; Molecular Dynamics; Binding free energy; Linear Interaction Energy; Free Energy Perturbation; Insulin-Regulated Aminopeptidase; Angiotensin IV; Oxytocin; Vasopressin; HA08; Aryl sulfonamides; HFI compounds.;

   Sammanfattning : In recent years insulin-regulated aminopeptidase (IRAP) has emerged as a new therapeutic target for the treatment of Alzheimer’s disease and other memory-related disorders. So far, many potent and specific IRAP inhibitors had been disclosed, including peptides, peptidomimetics, and low-molecular-weight sulfonamides. LÄS MER

3. 2. Challenges in Computational Biochemistry: Solvation and Ligand Binding

   Författare :Jens Carlsson; Johan Åqvist; Chris Reynolds; Uppsala universitet; []
   Nyckelord :Molecular biology; computer simulations; molecular dynamics; solvation free energy; Generalized-Born; Poisson-Boltzmann; ligand binding; binding free energy; linear interaction energy; binding entropy; hydration entropy; Molekylärbiologi;

   Sammanfattning : Accurate calculations of free energies for molecular association and solvation are important for the understanding of biochemical processes, and are useful in many pharmaceutical applications. In this thesis, molecular dynamics (MD) simulations are used to calculate thermodynamic properties for solvation and ligand binding. LÄS MER

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

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

   Sammanfattning : 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. LÄS MER

5. 4. 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

7. 5. Non-Steroidal Anti-Inflammatory Drugs in Cyclooxygenases 1 and 2 : Binding modes and mechanisms from computational methods and free energy calculations

   Författare :Yasmin Shamsudin Khan; Johan Åqvist; Hugo Gutiérrez de Terán; Xavier Barril; Uppsala universitet; []
   Nyckelord :TEKNIK OCH TEKNOLOGIER; ENGINEERING AND TECHNOLOGY; molecular dynamics simulations; binding free energy; molecular docking; cyclooxygenase; non-steroidal anti-inflammatory drugs; free energy perturbation; potentials of mean force;

   Sammanfattning : Non-steroidal anti-inflammatory drugs (NSAIDs) are one of the most commonly used classes of drugs. They target the cyclooxygenases (COX) 1 and 2 to reduce the physiological responses of pain, fever, and inflammation. Due to their role in inducing angiogenesis, COX proteins have also been identified as targets in cancer therapies. LÄS MER