Search for dissertations about: "molecular mechanics MM"

Showing result 1 - 5 of 23 swedish dissertations containing the words molecular mechanics MM.

2. 1. A multivariate approach to characterization of drug-like molecules, proteins and the interactions between them

   Author : Anton Lindström; Anna Linusson; Fredrik Almqvist; Anders Karlén; Umeå universitet; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; binding affinity; prediction; CAMD; principal component analysis PCA ; partial least squares projections to latent structures PLS ; MM-GB-SA; MM-PB-SA; docking; geometry optimization; protein secondary structure characterization; implicit solvent; generalized-Born; Poisson-Boltzmann; molecular mechanics MM ; drug discovery; bindningsaffinitet; prediktion; dockning; geometrioptimering; sekundärstruktur; matematisk vattenmodel; generalized-Born; Poisson-Boltzmann; molekylmekanik MM ; läkemedelsdesign; principal komponent analys PCA ; partial least squares projections to latent structures PLS ; MM-GB-SA; MM-PB-SA; Other chemistry; Övrig kemi;

   Abstract : En sjukdom kan många gånger härledas till en kaskadereaktion mellan proteiner, co-faktorer och substrat. Denna kaskadreaktion blir många gånger målet för att behandla sjukdomen med läkemedel. För att designa nya läkemedelsmoleyler används vanligen datorbaserade verktyg. READ MORE

4. 2. 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

5. 3. Luminescence properties of flexible conjugated dyes

   Author : Jonas Sjöqvist; Patrick Norman; Mikael Lindgren; Jacob Kongsted; Linköpings universitet; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; force field; molecular dynamics; linear absorption; QM MM; absorption spectrum; emission spectrum; water solvation; stokes shift;

   Abstract : In this licentiate thesis the luminescence properties of two flexible conjugated dyes have been studied. The first, Pt1, is a platinum(II) acetylide chromophore used in optical power limiting materials. READ MORE

6. 4. Theoretical studies of porphyrin proteins

   Author : Emma Sigfridsson; Beräkningskemi; []
   Keywords : NATURVETENSKAP; NATURAL SCIENCES; molecular mechanics; quantum chemical calculations; electrostatic potential charges; atomic charges; ferrochelatase; cytochrome; myoglobin; Porphyrin; haem; QM MM; reorganisation energy; Theoretical chemistry; quantum chemistry; Teoretisk kemi; kvantkemi;

   Abstract : Different aspects of porphyrin proteins have been studied with theoretical methods. For example, we have studied: - The importance of hydrogen bonds for the discrimination between carbon monoxide and molecular oxygen by myoglobin, the oxygen carrier in muscles, modelling the active site both in vacuum and in the protein matrix - The inner-sphere reorganisation energy during electron transfer for cytochromes compared to other electron-transfer proteins, such as blue copper proteins and Fe-S clusters - The role of porphyrin distortions in the reaction mechanism of ferrochelatase, the enzyme that inserts an iron ion into protoporphyrin IX to make haem - The interaction between different metal sites in ferrochelatase In these studies we have used density functional theory, classical force field methods, and a combination of quantum chemistry and molecular mechanics. READ MORE

7. 5. 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